What each release of Sequences changed, newest first. The hosted service and the server edition run the same releases. Each release names the version of its search engine, the part that runs searches, and every search record names the engine version that ran it.
Sequences 0.74.0
· Search engine 0.20.0
Groundwork for several servers sharing one queue, a line on the Roadmap. Nothing changes for a server as it runs today.
A restart still ends unfinished jobs, and you submit them again. The install guide will describe the settings for several servers when that work is ready.
Sequences 0.73.0
· Search engine 0.20.0
Cases read the changes a claim allows, such as "one, two or three amino acid substitutions", and the letters a claim reads as any residue, and rank and filter matches by them.
New: the case's rules find two more kinds of claim feature. Allowed changes reads a bounded count, such as "with one, two or three amino acid addition, deletion and/or substitution" or "up to 3 conservative substitutions", linked to the SEQ ID NO it changes. Letters read as any residue reads a claim's own definition, such as "wherein X is any amino acid and Z is any amino acid".
An open count ("one or more substitutions"), a lower bound ("at least three differences") and a change at a named position give no feature. In Review you can add or edit either kind by hand, as any other feature. See Cases: claims to search plan.
References: a match meets a claim that allows changes when its changes of the kinds the claim names, such as substitutions, number that many or fewer and it makes no change of another kind. A claim of "mutations" or "changes" counts every kind, and query letters outside the alignment count as deletions. Where the claim gives an identity too, either one meets it.
The Meets column reads "More changes" for a match with more, and "Other changes" for one with a kind the claim does not allow. The words count each kind: "Meets up to 3 substitutions: 1 substitution, 93.3% identity over the full query". Sequences does not check whether a substitution is conservative, and says so: "2 substitutions, not checked as conservative".
A letter a claim reads as any residue matches any residue in that claim's references, so a Z the claim defines as any amino acid no longer counts as E or Q there. See The References step.
Plan: a search for a SEQ ID NO whose claims allow changes keeps the identity those changes leave, and its reason says so, such as "Keeps 80% identity or more, which 3 changes leave in the 15 letters of each." Sentence 2 of "Why each reference counts" says it for the claim, with the kinds of change the claim allows.
Cases that exist keep their features. The rules find the new kinds in a set of claims you import or make current from now on, and you can add them by hand. A summary's facts change only for a feature of either kind, so every other decision holds.
For programs: POST /api/cases/{id}/features takes changes and wildcard, a reference group's threshold gives changes and wildcards, and a reference's best match gives its changes and changesByKind. The decisions file gives each new feature's details, such as "Up to 3 substitutions only". The OpenAPI description gives every field.
Sequences 0.72.1
· Search engine 0.20.0
A fix to cases: a query's X reads as any amino acid, as a sequence listing defines it, and a drafted plan's identity filter keeps the matches its claims cover.
Fixed: in a case's references, a match reads the query's letters as a sequence listing defines them. An X in a protein stands for any amino acid, so a reference that differs from a SEQ ID NO only at an X meets the claim as written: "Meets as written: 93.3% identity over the full query, and 1 position is X, read as any amino acid". See The References step.
The same goes for B, Z and J in a protein, and for N and the other IUPAC codes in DNA and RNA, such as R for A or G: each covers the residues WIPO ST.26 gives it, so Z covers E and Q. The search's own identity and Query Match do not change.
Fixed: a drafted plan's identity filter could hide matches its claims cover, since a search counts a query's X as a difference. A search for a SEQ ID NO that holds such letters now keeps less identity, by what those letters take away, and its reason says why, such as "Keeps 70% identity or more, since identity counts 3 of the 15 letters of each, X and Z, as differences."
A locked plan keeps its filters. To take the new rule, unlock the plan with a reason and draft it again.
Sentence 2 of "Why each reference counts" now says why such a search used less identity than its claims recite, such as "Claim 1 recites 90% identity or more; this search used 78%, since identity counts 1 of the query's 9 letters, X, as a difference." See Why each reference counts.
Where a best match now reads differently, because its query holds such a letter, the reference's summary has new facts, so it asks you to decide again. Every other summary keeps its facts and your decision.
Fixed: while an unlocked plan still held the searches of an older set of claims, the plan listed a fault for each search that pointed past the current claims' words. It now lists only "Draft the plan again: it was drafted for set 1, and set 2 is current.", since drafting again mends those faults too.
Sequences 0.72.0
· Search engine 0.20.0
Patent DNA and Patent proteins now hold US published applications, from the first in March 2001 to this week, with US patents from the same weekly files.
New: Patent DNA and Patent proteins hold US published applications, from the first, published 15 March 2001, to 12 November 2026: 288 thousand applications with sequence listings and 219.6 million SEQ IDs, 172.1 million of them DNA or RNA and 47.5 million protein. They come from the US patent office's weekly full-text files and published sequence listings. See Sets.
US patents granted since 2001 come from the same weekly files, so a new grant does not wait months for GenBank. An application and the patent granted from it share one sequence line when their letters match, so one hit lists both, each with its own dates.
Patent DNA now holds 74.9 million distinct sequences, up from 28.8 million, and Patent proteins 17.7 million, up from 10.5 million, from 826 thousand publications. A search you ran before keeps the snapshot it ran on.
A hit on an application shows its number, kind code, publication date, applicant and title, with its filing date and earliest priority date beside them. With Published before set, a sequence first published after your date still passes when a US application holding it was filed, or claims priority, before your date. See Dates.
Each week's applications and grants arrive as an addition to the snapshot: choose Main plus New under Collection to search them.
Smith-Waterman and global alignment read every stored sequence, so a DNA search of the larger Patent DNA takes longer: a 21-base Smith-Waterman query took 54 seconds on the hosted service. See Search methods.
The listings of 195 applications, which their weekly files name but the sequence listing site has not given yet, are not in the sets. Each weekly addition asks for them again.
Sequences 0.71.0
· Search engine 0.20.0
For a server you run yourself, a new guide page shows which NIST SP 800-53 controls of the moderate baseline Sequences meets, which your environment meets, and which the two share.
New for a server you run yourself: NIST SP 800-53 controls, a page of the guide Run Sequences on your own server. It takes each of the 146 controls and enhancements that the SP 800-53 Rev. 5 moderate baseline selects in access control, audit, configuration management, identification and authentication, system and communications protection, and system integrity.
Each row says whether Sequences meets the control, your environment meets it, or the two share it, and names the feature, setting, file or guide section that does. The page lists the baseline's source, NIST's OSCAL files with their commit and SHA-256 hashes, so you can check the list.
Sequences does not encrypt the files it stores, so protection at rest comes from your environment, such as an encrypted volume. Each file it writes is readable only by the service's account.
Sequences 0.70.0
· Search engine 0.20.0
Smith-Waterman and global alignment search DNA too, on both strands, and the status bar counts the queries done and gives the time left.
New: Smith-Waterman, Global on the query and Global on both sequences search a DNA set with a DNA query, on both strands, as they do protein. In our benchmark on Patent DNA, Smith-Waterman found 16 of 20 DNA fragments of 21 to 50 bases at 80% identity, where BLAST found 8. Automatic still runs BLAST for DNA. See Search methods.
Each DNA query reads every stored sequence, so a search takes minutes: on Patent DNA a Smith-Waterman query took about a minute at 21 bases and 5 minutes at 308 bases. The status bar counts the queries done and gives the time left in whole minutes, as in "2 of 5 queries done, about 6 minutes left". See While a search runs.
A DNA search whose estimate is longer than the server allows for one search, 60 minutes unless your organization set another limit, does not start, and the page says so with the estimate. Search fewer or shorter queries at a time, or use BLAST. POST /api/jobs and POST /api/estimate answer 400 with the same words.
A case's plan offers Smith-Waterman and global alignment for a DNA set too. For programs, a running Smith-Waterman or global search reports progress: the queries done, of all of them, and the part of the estimated work they hold.
Sequences 0.69.0
· Search engine 0.20.0
A Roadmap page lists the work planned for Sequences, by quarter.
New: the Roadmap page lists the work planned for Sequences by quarter, with what each release since 0.38.0 added. It opens from the row of pages at the top of the documentation and from the documentation home, without sign-in.
Expected in December 2026: US published applications in the patent sets, added each week, and Smith-Waterman and global alignment for a DNA query. Expected in March 2027: result files from other sequence search systems in a case, and several servers sharing one queue. Plans can change; these notes record what each release added.
Sequences 0.68.0
· Search engine 0.20.0
The query box, Open a file, a dropped file and the search API take PIR (NBRF) records as well as FASTA.
New: paste or drop PIR records, such as >P1;CRAB_ANAPL, wherever FASTA works: the query box, Open a file, a file dropped on the search card, POST /api/jobs and POST /api/batches. See Start a search.
A PIR header names the sequence after its semicolon, and its two letters give the type: P1 and F1 are proteins, and DL, DC, RL, RC, N1 and N3 are DNA or RNA. The line after the header describes the sequence, and the * that ends it is not searched.
The line beside the Query type chips says when a PIR header gave the type, and a chip that says otherwise is refused under the query box. A record without its closing * is refused too, so a FASTA name with a semicolon is never misread.
Fixed: a PIR protein record whose description held only letters was searched with those letters before its sequence. Import a database on the local workbench takes PIR files, and a case report prints a PIR query by its name and letters.
Sequences 0.67.0
· Search engine 0.19.0
A case keeps an application's claims as filed, as amended, as published and as granted, shows what changed between two sets, and carries your decisions over where a claim's words did not change.
New: each claims import in a case is a set of its own, as filed, as amended, as published or as granted, with its date. A publication's XML gives both. A new set becomes current unless it is dated before the current set. See Sets of claims.
The Claims step lists each set with its source and SHA-256, and Make current makes another set current, with an optional note for the log.
What changed compares any two sets claim by claim and marks each claim unchanged, amended, added or cancelled. Claims are matched by their words, so a renumbered claim shows its number in both sets. In an amended claim, added words are underlined and removed words are struck through.
When the current set changes, the rules find its features again. On a claim whose words did not change, even one renumbered, each feature keeps its decision, note and edit, including features the model suggested or you added. The model is not asked again.
A locked plan stays locked and follows the set it was locked on. To search the current set, unlock the plan with a reason and draft it again. The report names the set the plan follows, with its label, date, source and SHA-256.
New source: Word or text file, up to 15 MiB. In a Word file marked up as an amendment, struck-through text and tracked deletions are left out, and underlined text and tracked insertions are kept. In a claim marked "(Currently amended)", text in [[double brackets]] is left out, in pasted text too.
The decisions file names the set of claims behind each import, decision, model call and plan version, and lists each change of the current set with its note.
For programs: POST /api/cases/{id}/claims takes file, label, date and current, and GET /api/cases/{id}/claims/sets and GET /api/cases/{id}/claims/changes list the sets and what changed. The OpenAPI description gives every field.
Sequences 0.66.0
· Search engine 0.19.0
Admins can export the audit log of sign-ins, API tokens and starts, with every case's log, as JSON lines for a SIEM, and check its hashes with a script from the installation guide.
New: with sign-in on, the service keeps its own audit log on the data volume: each sign-in, refused sign-in, failed sign-in and sign-out, each API token made or revoked, each start with its settings, each change to the invite file and each audit export. See Audit export for a SIEM.
A secret in the settings shows only as set. The log holds no IP addresses, queries, sequences or results, and nothing rotates or rewrites it.
A failed sign-in is noted only when your provider's answer comes back to a sign-in this server started, so a call to /api/auth/callback from anyone else adds nothing. At most 30 failed sign-ins are noted a minute; past that, one event gives the count.
For admins: GET /api/admin/audit.jsonl?day=YYYY-MM-DD, or with from and to times, gives the audit log and every case's log for a UTC day or a time range as JSON lines. The container's audit-export command writes the same lines from the data volume, which it only reads.
Case events keep their IDs, counts and hashes and name each field they leave out, since claims pasted into a case can be from an application that is not yet published.
Each event carries the SHA-256 of the event before it and its own, and each log's lines end with the service's check of its whole chain. The installation guide's check_audit.py checks exports with Python 3 alone, across days, and against the data volume.
For programs: the OpenAPI description lists GET /api/admin/audit.jsonl.
Sequences 0.65.2
· Search engine 0.19.0
A fix to result-file imports: a FASTA36 36.3.8i file with comment lines imports into a case.
Fixed: a FASTA36 tabular file in -m 8 with its comment lines, from FASTA36 36.3.8i, imports into a case. Its comment lines name 14 columns, query length and subject length among them, but each row holds the usual 12, and Sequences refused the file at its first row. Sequences now reads the 12, and the import's warnings say so. See Result files from other programs.
On the command line, blastn runs megablast unless you add -task blastn, and megablast can miss weaker matches. The guide now says so: add -task blastn when a file should compare like for like with Sequences' own search.
Sequences 0.65.1
· Search engine 0.19.0
Cards, notes and selected rows show their state with a soft fill on rounded corners, not a colored edge down one side, and their words still say it.
Blocks that show a state now show it with a soft fill on rounded corners instead of a colored edge down one side: a claim feature in Review, the lock banner in Plan, a sentence in Why each reference counts, the broken event in Log, a CDR group of an antibody search and a note in these guides. Their words still say the state.
In the results list, a selected row and its pane no longer have a blue edge down their side: the row's tint and bold name show it. A chosen match in a pane fills with a stronger blue. The claim's words in Claims and References sit in a rounded box.
The clinical context and funding parts open with their lines set under the part's name, with no rule down their side.
Sequences 0.65.0
· Search engine 0.19.0
A case gives short summaries of its searches, its top references and each claimed SEQ ID NO, filled in from fixed templates and the case's own facts, and the report prints the ones you accept or edit.
New: summaries in a case. Claims gives each claimed SEQ ID NO's summary: the claims that recite it, and the paragraphs of the description that cite it, quoted. References gives a summary in each open row of the first 5 references and the ones you keep, and one for each search after the features. See Summaries.
No language model writes them. Each is filled in from a fixed template and the case's own facts each time you open it, so the same facts always give the same words. Each sentence names its source, and every number, date, SEQ ID NO and publication number in a summary is checked against those facts. A search's summary describes what the search returned, before your marks.
Choose Accept, Edit or Reject for each summary. An edit is one paragraph in your own words, and the draft stays beside them. Each summary names the template that filled it in, and a line in each step counts the summaries decided and the ones in the report.
When the facts behind a summary change after you decide, such as a new prior art date, the summary asks you to decide again and leaves the report until you do. The case log records every decision, and the decisions file lists each one with its template.
The report prints the summaries you accepted or edited in a new Summaries section after By applicant, each with the template that filled it in and who accepted it, and when.
A reference in a publication that no record names now reads "Publication unknown", with its sequence's accession, in References and its CSV.
For programs: GET /api/cases/{id}/summaries gives a case's summaries, and POST /api/cases/{id}/summaries/decisions accepts, edits or rejects one. The OpenAPI description lists their fields.
Sequences 0.64.1
· Search engine 0.19.0
A security update: the container image runs Node.js 22.23.5 in place of 22.22.1.
For IT staff: the image holds Node.js 22.23.5, the Node.js 22 security release of November 11, 2026. Nothing changes for people who search, and the install needs no new setting. See What you need.
Sequences 0.64.0
· Search engine 0.19.0
A case's decisions download as CSV and JSON, each tied to its event in the case log, and admins can measure the claim rules and model prompts across cases.
New: Download decisions (CSV) and Download decisions (JSON) in a case's Report step save every decision in the case: each claim feature, each accept, reject and edit with who made it and when, each model call with the suggestions kept or dropped and why, each sentence decision and the plan's versions. See The decisions file.
Each decision gives the number and SHA-256 of its event in the case log, so you can check the file against the log, and the JSON file gives the result of the log's check. An edit gives the finding before and after it. Saving the files changes nothing in the case.
For admins: GET /api/admin/decisions.csv and GET /api/admin/decisions.json give the decisions of every case by rule, kind, source, status, prompt and drop reason, with totals. They hold no claim words, quotes, notes or edits, since claims pasted into a case can be from an application that is not yet published. See Usage.
For programs: GET /api/cases/{id}/decisions.json and decisions.csv give a case's decisions, and the OpenAPI description lists their fields and columns.
Sequences 0.63.0
· Search engine 0.19.0
A case takes the result file of a search you ran outside Sequences, from BLAST+, FASTA36 or another program, and joins its matches to the stored patent sequences.
New: bring the result file of a search you ran outside Sequences into a case, under Import a result file in the Report step. Sequences joins each match to the stored patent sequences, and the file opens like one of your own searches, with marks, families, dates and explanations. See Result files from other programs.
It reads BLAST+ tabular, XML and JSON output, FASTA36 tabular output, and CSV files with a header row, the CSV files Sequences saves among them. A file can be up to 200 MB and 1,000,000 rows, and the page compresses it before sending it.
A match joins by its accession, or by publication number and SEQ ID NO however the number is written. A row that does not join is never dropped: Rows that did not join lists each with its reason, and Download them as CSV saves them.
A search of a copy of the patent sets on your own computer joins by each sequence's place in that copy, when the file names the copy's folder. BLAST+ XML, JSON and tabular output with comment lines name it, and so does FASTA36 tabular output with comment lines.
References combines an import's matches with your other searches by publication and SEQ ID NO, and the report names each imported file with its SHA-256, how many rows joined and the first rows that did not, each with its reason.
For programs: POST /api/cases/{id}/imports takes a result file as the request body, and GET /api/cases/{id}/imports/{jobId}/unresolved, or unresolved.csv, lists the rows that did not join. GET /api/status gives the limits and formats under imports.
Sequences 0.62.1
· Search engine 0.19.0
Two fixes to cases: a fragment length written in words reads as one number, and a model's entry in a case's Log keeps time order.
Fixed: in Review, a fragment length written in words reads as one number. "At least twenty-five consecutive residues" read as 5 to 20, "fourteen" as 4 and "seventy" as 7, and "at least 1,000 contiguous nucleotides" as 0 or more. Each now reads as the claim writes it. See Cases.
Fixed: "up to", "at most" and "no more than" give a longest length with no shortest one. "Up to 100 contiguous amino acids" read as 100 or more and now reads as written, and the plan gives "parts of up to 100 amino acids" as the search's reason.
In References, a claim's fragment length is the shortest alignment that counts for Meets. With the old reading, "at least twenty-five" let an alignment of 5 count; it now needs 25. A length with no shortest one, such as "up to 100", sets none, so identity counts over the whole query. See The References step.
Cases you already have keep their findings, plans and References as they were. To correct a length in an older case, choose Unlock the plan, then edit the finding in Review. Claims you import from now on are read the new way.
Where the server offers model suggestions, a model's entry in a case's Log now shows the time the model answered, so the Log stays in time order. Model suggestions stay off unless the server's operator names a model.
Sequences 0.62.0
· Search engine 0.19.0
On a server you run, the search page and the admins' usage page name the license by its plan and last day, such as "Evaluation license, ends 2027-02-28".
On a server you run, the search page's footer names the license by its plan and last day, such as "Evaluation license, ends 2027-02-28". It reads "starts" before the first day and "ended" after the last. See The license file.
For admins: the usage page opens with the same line. From 60 days before the end it adds the license's message, in amber, and once new searches stop it turns red. See Usage.
The installation guide says what an evaluation license covers and how it ends: read-only, as after a trial, so results stay open and new searches need a new license file.
For programs: the license in GET /api/status, and in GET /api/admin/usage for admins, has a label with the plan and the day the license ends.
Sequences 0.61.0
· Search engine 0.19.0
Paste a query or drop a file, and the search page reads what it is and where it goes.
New: Query type reads DNA / RNA or Protein from what you paste, and Search in follows it: the query's own sets first, then the other type's under Translated search. A click on a chip sets the type yourself. See Query type.
The search-type buttons are gone. Antibody CDRs is now a switch beside the search card's title.
A fault in the query shows under the box, names the line and the character, and selects it when you run the search.
Drop a file on the search card, or choose Open a file: FASTA fills the query box, a sequence listing opens its SEQ ID NO picker, and a publication's XML with claims starts a case with its claims and its listing. See Drop a file.
A finished search opens its result by itself, unless you opened another result or are typing in a field. The tab's title says Running or Done until then, and after a reload the status bar follows your newest search. See While a search runs.
Each result has an address that opens it again for your account. Copy link copies it, and Back closes the result. See Addresses.
Recent jobs has Find a search, by name or set, and a status choice.
A result with no match offers next steps, each a button that fills the search form. See No match.
Sequences 0.60.0
· Search engine 0.19.0
Review can ask a language model your server runs for claim features the rules missed, with the details a search needs and the paragraphs of the description that bear on the claims.
New: where the server's operator names a language model, Review can ask it for claim features the rules missed. The button reads "(Pilot)", and each suggestion counts only once you accept it. Suggestions stay off until a model is named. See Claim suggestions from a model.
A suggestion can carry the details a search needs: SEQ ID NOs, an identity threshold, a range of positions or a fragment length. Each number must be written in the claim's own words, or the details are dropped and the suggestion kept. Accepted with details, a suggestion drafts a search as a rules finding does.
When claims come from a publication's XML, the case also reads the description's numbered paragraphs. The model gets up to 40 of them that cite a SEQ ID NO the claims name or define a term the claims use, 60,000 characters at most, and a suggestion may quote the paragraph it draws on.
A model on processors can take minutes for one case. The call runs on the server while you keep working, the step shows how long it has been asking, and the notice says what it brought. The server asks the model for one case at a time.
Each call is recorded in its case, whether it brings suggestions or fails: the request as sent and its SHA-256, the model's answer, how long it took, and each suggestion kept or dropped with the reason. The case's log names each call.
For IT staff: BIOSEQUENCE_CLAIMS_MODEL_API=openai-chat sends a chat completions call, the format vLLM, llama.cpp's server and Ollama take, and the service waits up to 900 seconds for it unless BIOSEQUENCE_CLAIMS_MODEL_SECONDS says otherwise. See Claim suggestions from a model.
For programs: POST /api/cases/:id/suggestions with background: true answers at once, and GET /api/cases/:id/suggestions reads the call's state until it ends. Without background the request waits for the answer, as before.
Sequences 0.59.0
· Search engine 0.19.0
A case lists every reference its searches found under the claim feature that found it, ranked by fixed rules, in a new References step.
New: a case's References step, between Run and Report, lists every reference the case's searches found under the claim feature whose search found it, with the claim's words and its threshold. See The References step.
Inside a feature, references rank by fixed rules, with no language model: whether the best match meets the claim's threshold over the whole query, how much of the claimed region it covers, its date against the prior art date, then Query Match and E-value. Each row shows its rank with each score beside it.
Open a row for its scores in words, such as "Meets 90%: 97.3% identity over the full query", the search that found its best match and Open results. A feature with many SEQ ID NOs says how many each reference matches, such as "Matches 37 of 250 SEQ ID NOs".
Show excluded lists the references that every search that found them excluded, and Download CSV saves every reference of every feature with its scores.
For programs: GET /api/cases/:id/references gives the same list, one feature at a time with feature, offset and limit, and GET /api/cases/:id/references.csv the CSV.
Sequences 0.58.0
· Search engine 0.19.0
The same service as 0.57.0, with a fix in a tool only ConductScience runs: the build of Patent DNA and Patent proteins goes on when the patent office's sequence listing service fails for a publication.
When the patent office's sequence listing service answers a publication with a server error, the build of Patent DNA and Patent proteins goes on without it and counts it. A later update asks for it again and adds its sequences once the service sends them. A publication whose listing is printed in the publication itself keeps it meanwhile.
Sequences 0.57.0
· Search engine 0.19.0
One search can cover several sets: check them under Search in, and the result opens on one list of references.
New: Search in takes several sets. Check two or more, up to 8, and they run as one combined search, with one status bar and one result. A new search starts with its type's sets checked, apart from TrEMBL and NCBI core_nt, which take minutes. See Search several sets at once.
For a DNA or protein query, Translated search lists the sets of the other type, so the same search can read a protein in Patent DNA, in all six frames.
A combined search opens on References: each patent or database entry once, with its best match across the sets and a chip for each set that found it. Found in and Kind filter the list, and Keep or Exclude marks a reference in every search that found it.
Choose a reference to see its matches by set and query, each one click from its alignment. Search record lists each set's search with the SHA-256 of its record, and opens that search by itself.
For programs: GET /api/jobs/:id/hits/:row gives one hit of a search by its row number, with its mark. See Programs and API tokens.
Sequences 0.56.0
· Search engine 0.19.0
The listing import reads the sequence listing inside a patent publication's full-text XML, and programs can find jobs by name, set or state.
New: Import in the Listings tab of Sequence tools takes a patent publication's full-text XML when its listing is inside it, as in publications of 2001 to 2004, and reads that listing. A publication whose listing was filed separately says so. See Listings and the ST.26 check.
If an entry of such a listing cannot be read, it is left out and the listing's facts name it, such as "SEQ ID NO: 3 could not be read". The other entries import and search as usual.
For programs: GET /api/jobs takes text, to find jobs by name or by the set or database they searched, and status, one or more states separated by commas. GET /api/jobs/:id/request gives the request a search was started with. See Programs and API tokens.
Sequences 0.55.1
· Search engine 0.19.0
A fix to sample results: a sample added, removed or replaced while the service runs now shows at once on every server.
Fixed: on a Linux server, a sample result added, removed or replaced a moment after another change could keep showing as it was until the next change. Each change now shows at once. See A sample result.
For IT staff: sample add and sample remove now write a small .generation file in the samples folder after each change. Leave it there; the service reads it to see the change. See Sample results.
Sequences 0.55.0
· Search engine 0.19.0
Sample results: real searches of public sequences, saved and shown read-only, that anyone can read before signing in, linked from the sign-in page.
New: sample results you can read before signing in. Each is a real search of a public sequence, such as GLP-1 against Patent proteins, saved and shown read-only, with its patents grouped by family and each row opening to its best alignment. See A sample result.
The sign-in page says "Not ready to sign in? See a sample result." when a server has one. A sample takes the Patents tab's choices: families or every publication, its sorts, and Published before, which folds the later publications and counts them.
For IT staff: sample add makes a sample from a finished search of a patent set, and sample list and sample remove manage them. Anyone who can reach the server can read a sample, so use searches of public sequences. See Sample results.
Sequences 0.54.0
· Search engine 0.19.0
The search page now offers suggested searches: real public sequences, such as GLP-1 and human insulin's gene, that run with one click and show what to try in their results.
New on the search page: Suggested searches, real public sequences you can search with one click. GLP-1 against Patent proteins, human insulin's gene against Patent DNA, green fluorescent protein against Patent DNA read as protein, the antibody trastuzumab by its CDRs, and the peptide SIINFEKL as exact text. See Suggested searches.
Run fills the form as you would and starts the search, and its result opens when it finishes. Edit first fills the form and leaves the search to you. Each card links the public record its sequence comes from.
The result of a suggested search shows Things to try: two or three steps that use it, such as setting a prior art date. Close hides them for that search in this browser.
The panel is open until your first search, then folds to one line. Try a suggested search, at the top of the page, opens it.
Sequences 0.53.0
· Search engine 0.19.0
Patents now groups publications by patent family, marks a family as one, and folds the publications after your date into one line under the list.
On Patents, the new Group choice sets what a row is. With Families, each row is one patent family: the publications that share a priority claim or an application, or the same title and applicant where no priority claim is on record. The row shows the earliest publication, the family's best measures and a chip such as "+2 in family". See By patent.
The line over the list counts both, such as "12 publications in 5 families match these filters." Every publication lists one publication a row, as before. Applicants and a case's report count publications whatever Group says, and Export matches saves one row for each publication.
A family's pane says how the family was formed, lists its publications earliest first with their dates and an Open link, and shows the chosen publication's matching sequences with the best alignment.
Keep and Exclude on a family row mark each of its publications in the list at once. The Mark column says "Kept" when the whole family is kept and "Some kept" when only part of it is. To mark one publication of a family, choose Every publication. See Keep and exclude.
With Published before set, Patents keeps the publications from before your date, the US and WO publications filed or claiming priority before it, marked "Filed before", and the undated ones. The later publications of the same sequences fold into one line under the list, and Show them brings them back, marked "After date". See Dates.
A Smith-Waterman or global alignment search that reaches its limit now says on the page that its list holds the best-scoring sequences, and that Exact text finds every exact occurrence.
Sequences 0.52.0
· Search engine 0.19.0
Programs can now run one search across several sets and get one list of what they found, where a patent or database entry that several sets found is one row.
In the API, POST /api/groups runs one search across 2 to 8 sets, such as Patent proteins, Patent DNA and Swiss-Prot. Every set is checked first: if one cannot take the query, or the queue lacks room, none starts and the answer says why. See Programs and API tokens.
GET /api/groups/{id}/references gives one list for a combined search. A patent or database entry that several sets found is one row, with its best measures, its earliest date, the sets and queries that found it, and each match. It takes the filters, sorts, families and date fold of a search's patents, plus set and kind.
The list answers while some sets are still running and says which searches it holds. GET /api/groups/{id} gives each search's state, matches and time left.
POST /api/groups/{id}/marks keeps, excludes or clears up to 500 references at once, in every search of the combined search that found them, so each search's own lists show the mark.
GET /api/groups/{id}/references.csv has one line per reference, with a sets column and the family columns. POST /api/groups/{id}/again runs a combined search again, all of it or only the sets you name, and DELETE /api/groups/{id} stops its searches still waiting or running.
Only the account that made a combined search can see or change it. Combined searches are in the API only for now; the page shows them in a later release.
Sequences 0.51.0
· Search engine 0.19.0
Search results are now a list of one-line rows beside a detail pane, so you can read a result, mark it and move to the next without leaving the list.
On Patents and Alignments, each result is one line. Select a row to see all of it in its pane: on a wide screen the pane sits beside the list and each scrolls on its own, and on a narrower screen the pane opens under the row. The row you select stays where it is on the screen. See Results.
Keys work while the list has the focus: Up and Down move, Page Up, Page Down, Home and End jump, K keeps, X excludes, U clears, R goes to the reason field, Esc comes back and C copies the alignment. Keys, above the list, lists them.
The pane shows the alignment 60 letters to a line, with each letter of the hit that differs from the query in bold. Copy alignment and Download .txt give it as text.
A patent's pane lists its matching sequences by SEQ ID NO and opens on the best one's alignment. Choose another sequence to see its alignment.
An alignment's pane lists where its sequence is published, earliest first, and links each database entry that holds it to its record at UniProt or ENA.
Keep, Exclude and Clear are in the pane, beside Reason (optional). To give a marked row a new reason, type it and press Enter. See Keep and exclude.
In the API, GET /api/jobs/{id}/hits takes publication for the hits of one publication, and GET /api/jobs/{id}/publications takes row for every publication of one row's sequence. See Programs.
Sequences 0.50.0
· Search engine 0.19.0
A case now keeps its application number and prior art date, a plan can search every set on the server, and a plan of any size runs to the end by itself.
A case keeps its Application number and Prior art date. A publication's XML fills them in, and when it gives an earliest priority date you can choose that date instead. Change in the case's header edits both. See Cases.
New plan searches look for what was published before the case's prior art date, and the date sentence under Why each reference counts names the date it uses. A locked plan version keeps the date it was locked with.
A drafted plan searches every set on the server that holds the finding's type, the patent sets first: for a protein, Patent proteins and Swiss-Prot. Set to search lists every set, from any snapshot on the server, and each attached database.
TrEMBL and attached databases such as core_nt join a plan only when you ask: a button such as Add TrEMBL adds a copy of each fitting search and says how long they should take.
Any locked plan runs, however many searches it needs. The case starts what the queue has room for, keeps 2 places for searches from the form, starts the rest as searches finish, and goes on by itself after the server restarts.
Each run shows a line such as "7 of 12 searches done, about 4 minutes left." A search that failed, was cancelled or was interrupted has Run this one again.
The case report adds the application number and prior art date, a table of the plan's searches and the features no search covered.
In the API, PATCH /api/cases/{id} takes applicationNumber, priorArtDate and priorArtDateBasis, and GET /api/cases/{id}/runs gives each run's progress. On a server you run, BIOSEQUENCE_MAX_JOBS sets how many searches the queue holds. See Settings.
Sequences 0.49.0
· Search engine 0.19.0
Publications that tie now list the earliest first, the date filter keeps a sequence whose US or WO publication was filed before your date, and programs can list a search's patents by family.
On Patents, publications that tie on the sort now go earliest first, undated last, so among the publications with the best Query Match the earliest is on top. Under the earliest or latest date, publications of one date go highest Query Match first. See Filters and sorting.
On Alignments, rows that tie go by their sequence's first published date, oldest first. Before this release, ties on both tabs went by publication number or row number.
Published before now also keeps a sequence first published on or after your date when one of its US or WO publications was filed, or claims priority, before it, where the record gives those dates. Its publications from on or after your date are still marked "Published on or after your date". See Dates.
On Patents, Export matches (CSV) ends with four new columns: family, family_size, family_basis and date_group. See Exports and search records.
In the API, GET /api/jobs/{id}/publications takes group=family for one row per patent family and later=hide to fold the publications from on or after the date. Every patent row gives dateGroup, and a hit row kept by a filing or priority date carries filedBefore. See Programs and API tokens.
POST /api/jobs/{id}/marks and a case's marks route take ids, up to 500 publications at once, so a program can keep or exclude a whole family.
Family rows and the date fold are in the API only. The page still lists one row per publication.
Sequences 0.48.0
· Search engine 0.19.0
The funding trail can show what a hit's US published applications state about federally sponsored research, word for word, after its papers, on a server whose settings name the add-on and whose funding trail folder holds the statements.
On the Alignments tab, a muted line after a hit's papers names the statements on federally sponsored research of the US published applications that hold its sequence, earliest first. Under it, a closed part for each of up to three applications has the application's number and publication date for its summary. See Funding trail.
Opened, a part shows the statement word for word, under the heading the application puts above it, if there is one. A hit whose applications give more ends on a line that counts the rest. A statement that only says it does not apply is left out. The parts match no statement to an NIH award or to a paper's grants, and draw no conclusion.
An add-on runs only on a server whose settings name it, and a server that names none holds none of its data. The hosted service runs no add-ons.
On a server you run, the funding trail folder is now format 1.1.0 and can hold the statements, and each week a new release of the folder adds that week's applications. A folder of 1.0.0 still opens and shows none. Upgrade the image before you load a folder with statements: an older image loads it and shows none of them. See Funding trail.
In the API, where the folder holds statements, a hit row carries statements, at most three, each with publication, published, heading and paragraphs, and statementsMore when its applications give more. See Programs and API tokens.
Sequences 0.47.1
· Search engine 0.19.0
The same service as 0.47.0 under a new number. One of 0.47.0's own tests stopped its install on the hosted service, and this release fixes what it found, in a tool only ConductScience runs. The hosted service took 0.47.0's changes with this release.
Nothing changed for people who search, and a server that runs 0.47.0 does not need this release. The 0.47.0 notes list what both releases add.
Sequences 0.47.0
· Search engine 0.19.0
On Alignments, a patent hit names the applicant of its earliest publication. The CSVs gain that publication and a patent publication's filing date, application number and priority claims, and the case report a Filed column, where the records give them.
On Alignments, a line under a patent hit's title names the applicant of the publication the title names, the sequence's earliest. Export matches (CSV) ends with that publication: first_publication, first_kind, first_applicant, first_filed, first_application_number and first_priority. See Exports and search records.
On Patents, the CSV ends with application_number, filed and priority. A priority cell lists every claim a record gives, earliest first, each as a date and a number.
Where a publication's record gives its filing date or priority claims, its row on Patents shows them beside the publication date, and the case report adds a Filed column. They do not change its date. The records in the patent sets give neither. See Dates.
In the API, a hit row has firstPublication and a publication row has applicationNumber, filed and priority. See Programs and API tokens.
Sequences 0.46.0
· Search engine 0.19.0
The funding trail, a second add-on: under each paper of a hit, the grants PubMed lists for it, with the NIH awards they match, on a server whose settings name the add-on.
On the Alignments tab, a paper under a hit whose grants PubMed lists has a closed Funding part. Opened, it shows each NIH award the paper's grants match: the project number linked to NIH RePORTER, the title, each institution with its fiscal years and the investigators NIH lists. See Funding trail.
The paper's other grants follow as PubMed lists them: other funders, contracts and numbers that match no single NIH project. The part names its sources and their dates, shows no award amounts and draws no conclusion. Sources and terms has a card for them.
An add-on runs only on a server whose settings name it, and a server that names none holds none of its data. The hosted service runs no add-ons.
On a server you run, BIOSEQUENCE_ADDONS takes funding beside clinical, and BIOSEQUENCE_FUNDING names a funding trail folder from ConductScience, which load checks file by file. See Funding trail.
Sequences 0.45.0
· Search engine 0.19.0
Clinical context, the first add-on: under a protein hit that is a drug target, the drugs that act on it, the diseases they are studied for and their clinical trials, on a server whose settings name the add-on.
On the Alignments tab, a Swiss-Prot or TrEMBL hit whose UniProt entry is a drug target has a closed Clinical context part under its title. Opened, it lists the drugs that act on the target, highest clinical stage first, with each one's mechanism; the diseases each drug is studied for; and their trials, ten at a time. See Clinical context.
The target, the drugs and the diseases link to Open Targets, each drug also to ChEMBL, and each trial to ClinicalTrials.gov. The part names its sources and their dates and draws no conclusion from them. Sources and terms has a card for them.
Patent and EST hits, hits with no UniProt accession and antibody region searches show no clinical context.
An add-on runs only on a server whose settings name it, and a server that names none holds none of its data. The hosted service runs no add-ons.
On a server you run, BIOSEQUENCE_ADDONS and BIOSEQUENCE_CLINICAL turn it on with a clinical context folder from ConductScience, which load checks file by file. See Clinical context.
Sequences 0.44.0
· Search engine 0.19.0
A user guide, an installation guide and these release notes, served by every server for the release it runs.
The pages open without sign-in on the hosted service, on a server you run and on the local workbench, and the docs home names the release the server runs.
The User guide covers searches, results by patent, applicant and alignment, papers, dates, exports, watches, portfolio exports, cases, listings, antibody CDR search and API tokens.
The Installation guide is for the IT staff who run Sequences on your own server, or in your AWS account with the AWS install kit (beta).
On a server with its own sign-in, watches now send email to people who sign in with a verified email address, as the installation guide says. A watch saved before this release sends none until you watch its search again. See Watch emails.
Every page links to the docs from its footer.
Sequences 0.43.1
· Search engine 0.19.0
A search that found no patent publication, such as a search of Swiss-Prot, now opens on its alignments instead of on an empty Patents tab.
A search opens on Patents only when it found a patent publication, and otherwise on Alignments, with the Patents tab beside it. Searches run before this release open the same way. See Results.
Nothing else changed.
Sequences 0.43.0
· Search engine 0.19.0
The AWS install kit, a beta: one CloudFormation stack puts Sequences on a server in your organization's own AWS account. A server with sign-in also answers a load balancer's health check at its IP address, and every server keeps an idle connection open longer than an AWS load balancer does.
A CloudFormation template and kit.sh, the script its server runs, put Sequences on one server in your organization's own AWS account (kit 1.0.0). See In your AWS account (beta).
One stack creates a memory-optimized EC2 server with no public address and no key pair, encrypted gp3 disks, its security groups and its role, and, with sign-in, an HTTPS Application Load Balancer with your ACM certificate. The role can read only its folder of your bucket, the stack's settings and the secrets you name, and with ECR pull from one repository.
On its first boot the server installs Docker, gets the Sequences image from S3 or ECR, copies each snapshot from S3, loads it against its SHA-256 list and runs verify on it before the service starts. The stack completes only then.
You manage the server through Session Manager: kit.sh apply puts a stack update in place, and kit.sh check checks the install. ServerPolicyArns gives the server's role your own policies from its first boot, PatentLink sets or removes the link on each patent number, and AddOns takes only none: kit 1.0.0 runs no add-ons.
The kit runs 0.43.0 and later. It is a beta: it has been tested against stand-ins for the AWS services, not yet in an AWS account, and it drops "beta" once a test install in an AWS account passes its guide's checks.
With sign-in on, GET /api/health also answers at the server's IP address, because a load balancer's health check cannot name the host. It still says only whether the service can search. Any other path, or a host name that is not allowed, still gets 403. See Health and logs.
Every server keeps an idle connection open for 65 seconds, longer than an AWS load balancer's 60.
Nothing changed for people who search.
Sequences 0.42.0
· Search engine 0.19.0
Applicant watches and portfolio exports: a watch can follow an applicant as well as a search, one applicant's publications export with their sequences, and the case report lists the kept results by applicant.
Each named row of a snapshot search's Applicants tab has Watch this applicant, and Your watches has a Watch an applicant form that takes a name. The watch follows the applicant on its snapshot, with the names your account has joined to it. A watched row reads Watching, which goes to the watch. See Watches.
After each weekly addition, a watch on an applicant lists the applicant's new publications under Your watches, each with its date and number of sequences, linked to the patent. It runs no search. On a server with watch emails set up, the new publications also go to your email. The hosted service sends no watch emails.
Your watches now shows whenever the server has a patent snapshot, so the form is there before your first watch.
Export portfolio, on an Applicants row or on a watch, starts a job in Recent jobs. It collects every publication in the snapshot and its weekly additions whose first-named applicant is the applicant or a name you joined to it, with each of their sequences in Patent DNA and Patent proteins, as a CSV file and a FASTA file. See Portfolio export.
An export holds up to 100,000 sequences and 100 million letters, oldest publications first, and says how much of the applicant it holds. Its files download from the row or from the job's card.
The PDF and Word reports of a case have a new By applicant section after the table of searches. It groups the publications you kept, and the publications that hold each kept match, by applicant across all of the case's searches, with your joins.
For programs, POST /api/watches also takes an applicant, and POST /api/portfolios, GET /api/jobs/{id}/portfolio.csv and GET /api/jobs/{id}/portfolio.fasta are new. All are in the OpenAPI description.
On a server you run, a portfolio export counts toward BIOSEQUENCE_CONCURRENCY, stops at BIOSEQUENCE_JOB_SECONDS and keeps its files with its job, about 250 MB at its limit. It needs no new setting. After a license or trial ends, no watch or export starts. Finished exports still download, and watches can still be paused or deleted. See Settings.
Sequences 0.41.0
· Search engine 0.19.0
Why each reference counts: a case drafts short sentences on why each publication it keeps bears on the claims, from facts it has stored, and you accept, edit or reject each one.
For each publication you keep, and for the top 5 publications of each search, the case drafts up to four sentences: the best alignment, the claim's identity threshold that the search used, the publication date against the filing date, and the genes and diseases named by the paper that reports the sequence. See Cases.
Each sentence comes from a fixed template and names its source, with a link to it: the result row, the plan version, or the publication's or paper's page. No language model writes them, so the same facts always give the same words.
Under Why each reference counts in the Report step, accept, edit or reject each sentence. The PDF and Word reports print the accepted and edited sentences of the publications you keep, with their sources. The case log records each decision, and an edit keeps both the draft and your words.
When the facts behind a sentence change after you decide, the sentence says that its draft changed, and it leaves the report until you decide again.
Once a license or free trial has ended, a new decision is refused. The drafts and decisions can still be read, and reports still made.
Two fixes to the PDF and Word reports. Since 0.32.0, a case whose claims came from a publication's XML file printed "[object Object]" in the Claims row, and the row now names the publication. Where an event in the report's case log quotes a SHA-256, the report now prints its first 12 characters, so the line no longer wraps. The case keeps the full value.
For programs, GET /api/cases/{id}/explanations lists the drafts and decisions, and POST /api/cases/{id}/explanations records a decision. Both are in the OpenAPI description.
On a server you run, no setting and no stored data change, and existing cases get drafts from what they already hold. The paper sentence needs a paper folder made with PubTator 3, which the papers command of 0.40.0 already takes. A folder made without it must be made again, with a new ID for BIOSEQUENCE_PAPERS. See Paper citations and marks.
Sequences 0.40.1
· Search engine 0.19.0
The same service as 0.40.0 under a new number. Two of 0.40.0's own tests stopped its install on the hosted service, and this release fixes them. The hosted service took paper citations, paper dates and retraction marks with this release.
Nothing changed for people who search, and a server that runs 0.40.0 does not need this release. The 0.40.0 notes list what both releases add.
Sequences 0.40.0
· Search engine 0.19.0
Each paper on a hit reads as its PubMed citation, is dated by the day it first came out, and says whether it was retracted, drew an expression of concern or was reinstated.
The hosted service never ran this release. It took these changes with 0.40.1.
Each paper under a hit reads as a full citation, with links to its PubMed record and its DOI. See Papers.
A paper is dated by the day PubMed says it first came out, online or in print, whichever came first. Published before compares days, so a hit whose only paper came out in December 2015 no longer passes a date of June 1, 2015. See Dates.
A paper that was retracted, drew an expression of concern or was reinstated says so under its citation, with the day, the notice and the source: PubMed, the Retraction Watch Database, or both. When no source gives the day, the mark says so. A paper whose PubMed ID was deleted keeps its year and says it is not in PubMed.
The CSV of the alignments adds paper_dates and paper_marks. The case report lists the papers of the matches you kept in the same way, and names the PubMed data each search used.
A search keeps the papers it had when it ran, so a search from before this release shows no marks. Run it again to see them.
For programs, each hit from GET /api/jobs/{id}/hits carries the same papers in paperList, with paperDates and paperMarks as in the CSV.
On a server you run, BIOSEQUENCE_PAPERS names a paper folder made with the new papers command from PubMed's files and the Retraction Watch Database. Without it, each paper keeps its year. See Paper citations and marks.
Sequences 0.39.0
· Search engine 0.19.0
Results by applicant: a new Applicants tab groups a search's patents by who applied, lets you join names that differ, and suggests the matching record in the Research Organization Registry (ROR).
A search of the snapshot has an Applicants tab beside Patents and Alignments. Each row is one applicant, the first applicant each publication names, with its publications, earliest date and best identity. See By applicant.
Spellings that differ only in case, accents, punctuation or a legal ending such as Inc or GmbH share a row. Publications with no applicant are listed under "Applicant not given".
Names that still differ, such as a company's old and new names, can be joined: select them and choose Join selected names. A join covers all of your searches until you undo it. Every join and undo goes into your account's join log, and Check the log verifies it.
Where an applicant's name matches an organization's name in ROR, the row links to its ROR record. A suggestion never joins or renames names. The hosted service suggests from ROR v2.15, data of October 20, 2026.
The filters work as on Patents, and Export matches (CSV) saves the rows as the screen shows them.
For programs, GET /api/jobs/{id}/applicants and GET /api/jobs/{id}/applicants.csv are in the OpenAPI description. Joins are made on the page only.
When a sequence listing gives its applicant's name in another script, such as Japanese or Korean, and also in Latin letters, new snapshots store the Latin form.
On a server you run, BIOSEQUENCE_ROR names a ROR name index made with the new ror command. Without it, the tab works with no suggestions. Joins are kept in applicants/ in the data volume, so back it up. See ROR suggestions.
Sequences 0.38.0
· Search engine 0.19.0
Programs can use Sequences: personal API tokens, batches of up to 100 searches, and an OpenAPI 3.1 description of the routes.
Signed in with a browser, open API tokens beside your account to make a named token, which the page shows once. A program sends it as Authorization: Bearer <token> and acts as your account, under the same rules.
A token lasts at most 90 days, and an account may have 10 live tokens. The page shows when each token was last used and lets you revoke it.
POST /api/batches starts 1 to 100 searches in one request. If any of them cannot run, none starts, and the answer lists each problem. GET /api/batches/:id gives the state of each search.
GET /api/openapi.json describes the routes a program uses. It is open without sign-in and holds no data.
On a server you run, BIOSEQUENCE_TOKEN_DAYS sets the longest a token may last, and 0 turns tokens off. Admins see every account's tokens on the usage page and can revoke any of them. See API tokens for programs.
Sequences 0.37.0
· Search engine 0.19.0
Hits show their papers and database entries, with dates, and two large public sets join the snapshot: UniProtKB/TrEMBL and the ESTs of the European Nucleotide Archive (ENA).
Under each hit's title the page says how many database entries and papers hold the sequence, and lists up to three papers, oldest first, each linked to PubMed or its DOI.
Database entries now keep the day their sequence became public, where it is known, so Published before uses a hit's earliest date across its patents, entries and papers. A paper is dated by its year only and counts as earlier than every day of that year, so the filter never hides a paper from the year of your date. See Dates.
TrEMBL and the ESTs are new sets. The ESTs come from ENA's files of September 10, 2026. Swiss-Prot entries now list their papers.
The hosted service also searches NCBI core_nt with BLAST. When ENA also holds a hit, the hit shows ENA's description and papers and, if that record is at version 1, its first public day.
TrEMBL and core_nt searches take minutes, so the page never selects them for you, and it says how long a search should take before you run it.
The CSV of the alignments ends with four new columns: entries, papers, pubmed_ids and dois.
A Smith-Waterman or global search of a whole set can return a slightly different list when it runs again, because its E-values come from a random sample of scores. BLAST, exact and pattern searches return the same hits each time.
The sets are listed in one order (patent DNA, patent proteins, Swiss-Prot, TrEMBL, ESTs), each from its newest snapshot. An older snapshot leaves the list, but a saved search, Run again or a watch still finds it.
Sequences 0.36.1
· Search engine 0.18.0
A change to how the hosted service is installed. Nothing changed for people who search.
Sequences 0.36.0
· Search engine 0.18.0
The hosted service moved to new servers at the same address. Pages, searches, settings and saved searches did not change.
Sequences 0.35.0
· Search engine 0.18.0
The Listings tab checks a WIPO ST.26 sequence listing before you file it.
The check reads the file against ST.26 version 1.7 in your browser, so the file does not leave your computer.
An error is a fault that WIPO Sequence 3.1.3 also rejects. A warning departs from the standard's wording or advice but passes.
Show every problem, errors only or warnings only, filter by SEQ ID NO, and download the problems as CSV.
Sequences 0.34.1
· Search engine 0.17.0
Changes to internal checks only. Nothing changed for people who search or for servers you run.
Sequences 0.34.0
· Search engine 0.17.0
A plans page and free trials on the hosted service.
The plans page lists the plans of the hosted service and the server edition, with their prices, and opens without sign-in.
On the hosted service, an account that was not invited starts a free trial at its first sign-in, on the terms the plans page gives. The search page shows the days left. When a trial ends, its searches stay open and no new search starts.
Sequences 0.33.1
· Search engine 0.16.0
No change to Sequences.
Sequences 0.33.0
· Search engine 0.16.0
Watches: a finished search of the snapshot runs again when the snapshot gets newer records, and shows only the matches it has not found before.
Choose Watch this search on a finished search. Your watches lists each watch with its state and its new matches.
Where the server sends email, new matches also go to your address, and each email has a link that pauses the watch without signing in.
A case's Report step downloads its searches, kept results and notes as a PDF or a Word file.
The server keeps no copy of a report. The case log records each report's SHA-256.
Sequences 0.31.0
· Search engine 0.14.0
A usage page for the admins of a server with sign-in.
Admins see a Usage link beside their account. The page counts searches and other work for each account and day over the last 7, 30 or 90 days.
Sequences 0.30.0
· Search engine 0.13.0
A health address for uptime monitors.
GET /api/health answers without sign-in: 200 when the server can search and 503 when it cannot. It says nothing else.
Sequences 0.29.2
· Search engine 0.12.2
An update of the hosted service no longer drops a page or stops a search.
Sequences 0.29.1
· Search engine 0.12.1
The query box takes a pasted sequence with no FASTA header.
Sequences 0.29.0
· Search engine 0.12.0
A My account link beside your account on the hosted service, for the settings of your ConductScience account.
Sequences 0.28.0
· Search engine 0.11.0
Antibody CDR search on the search page.
Paste up to 10 heavy or light chains and number them by Kabat, Chothia or IMGT, or type the CDRs in, then search the CDRs against a protein set.
Results group by patent or by stored sequence and show, for each CDR, an exact match, its identity or that it is missing. See Antibody CDR search.
Sequences 0.27.0
· Search engine 0.10.0
The server edition: Sequences as a container image that your IT staff run on your own server.
People sign in through your own OpenID Connect provider, such as Okta, Microsoft Entra ID or Keycloak.
A license file signed by ConductScience is checked inside the container. There is no license server.
Snapshot copies load with a SHA-256 check of every file, and each snapshot carries its sources and terms.
The service turns off the usage reports that BLAST+ can send to NCBI. See the Installation guide.
Sequences 0.26.0
· Search engine 0.9.0
Claims to search plan, and antibody numbering in the service.
A case imports claims and marks what each claim recites: SEQ ID NOs, identity thresholds, fragments, complements, CDRs and sequences written out in the claim. You review each finding, and the reviewed list locks as a search plan before any search runs.
The service numbers antibody chains by Kabat, Chothia or IMGT. The search page uses it from 0.28.0.
Sequences 0.25.0
· Search engine 0.8.0
Sequence listings, sequence tools, additions to the snapshot, and Run again.
The Listings tab reads a WIPO ST.26 or ST.25 sequence listing and searches its sequences.
The Editor, Fragments and Align tabs check, edit, save and align sequences.
A snapshot can take additions of newer records, and the Main plus New collection searches them with it.
Run again repeats a finished search with the same queries, settings and data.
Sequences 0.24.0
· Search engine 0.7.0
A new design, and the search page took the name Sequences.
The page serves its own font and loads nothing from another site.
Sequences 0.23.1
· Search engine 0.7.0
The hosted service moved to sequences.conductscience.org. The earlier address forwards there.
Sequences 0.23.0
· Search engine 0.7.0
The hosted service, for invited accounts.
Sign in with a ConductScience account. Each search belongs to the account that started it, and no other account can open it.
The hosted service searches the snapshot. Importing a collection of your own is for the local workbench.
Sequences 0.22.0
· Search engine 0.7.0
A fixed benchmark of searches checks each release, and the search record says that the E-values of Smith-Waterman and global alignment come from a random sample.
Sequences 0.21.0
· Search engine 0.6.0
Smith-Waterman and global alignment, and an automatic choice of method.
A snapshot search picks its method by the query, and the search record states the pick: Smith-Waterman for a protein, and BLAST with a full exact scan for DNA under 50 bases.
You can also choose Smith-Waterman or global alignment by name.
Align exactly aligns up to 1,000 chosen rows of a BLAST search again in full, by Smith-Waterman or global alignment, and adds the new scores to those rows and the CSV.
Sequences 0.20.0
· Search engine 0.5.0
Exact and pattern search. Both read every stored sequence, so their counts are complete.
Patterns take wildcards, gaps, repeats and IUPAC codes, and a DNA search covers both strands unless you pick one.
Each row gives the strand, how many times the text occurs and its first 20 positions.
Sequences 0.19.0
· Search engine 0.4.0
Results by patent and by date.
A snapshot search opens on its patents, each with its office, number, date, applicant and SEQ ID NOs.
Published before keeps a sequence first published before your date, and an undated sequence always stays.
Keep or exclude a patent or a row, with a reason. The CSV of the patents and the CSV of the alignments both carry the marks.
Past searches come in pages, and each search shows an estimate of its time.
Sequences 0.18.0
· Search engine 0.3.0
The sequence snapshot: GenBank's patent sequences, the patent proteins of EMBL-EBI and UniProtKB/Swiss-Prot in one read-only collection, each sequence stored once with every record and publication that holds it.
Sequences 0.17.0
· Search engine 0.2.0
Searches of large databases, such as the patent sequence sets.
Short queries, DNA under 50 bases and proteins of 30 residues or fewer, use BLAST's short-query settings automatically.
Each query says what it ran with and whether it reached the limit of 5,000 sequences.
Sequences 0.16.2
· Search engine 0.1.0
Documentation only. Nothing changed in the search.
Sequences 0.16.1
· Search engine 0.1.0
Documentation only. Nothing changed in the search.
Sequences 0.16.0
· Search engine 0.1.0
The first release: a local workbench that runs NCBI BLAST+ on your computer in all four directions between DNA and protein.
Import nucleotide or protein FASTA collections, run searches as jobs you can cancel, filter by identity, coverage and text, and export CSV and a full JSON record.
