User guide

Start a search

Sequences runs in three ways:

• The hosted service, at sequences.conductscience.org. Sign in with your ConductScience account.
• A server your organization runs, the server edition. Sign in with your organization's account.
• The local workbench: Sequences with sign-in off, on one computer, for one person. It needs no sign-in. See Sign-in off.

Open the search page, then:

1. Paste one or more sequences into Query sequences, or choose Open a file. Query type reads DNA / RNA or Protein from the letters; choose the other one if the reading is wrong.
2. Under Search in, check one or more sets, such as Patent proteins, and choose a search method. Two or more sets run as one combined search.
3. Give the search a Search name if you like, then choose Run search.

Search in lists the sets of the query's type first. Translated search, under them, lists the sets of the other type, unchecked; a search there reads the DNA in all six frames.

To search an antibody's CDRs, turn on Antibody CDRs beside the search card's title. The card then shows the antibody form, described under Antibody CDR search below.

The query box takes FASTA, with a >name line before each sequence, PIR records, or plain letters, which become one query named "query". It takes up to 20 queries, of up to 20,000 letters each and 100,000 in all. Spaces and digits are left out, and in RNA a U is searched as T. Reverse complement replaces each DNA query in the box with its reverse complement. Where no suggested search can run, Try an example query fills the box with a made-up DNA query.

A PIR (NBRF) record starts with a header such as >P1;CRAB_ANAPL, which names the sequence after the semicolon. The next line describes the sequence, and may be blank. The sequence follows and ends with *. The header's two letters say what the sequence is: P1 a protein and F1 a protein fragment; DL and DC linear and circular DNA; RL and RC linear and circular RNA; N1 and N3 other RNA, N3 for transfer RNA. With XX the letters decide. A file may hold several records, and FASTA and PIR records can share a query.

Each search runs as a job. Recent jobs lists your searches: open a finished one to see its results, or cancel one that is still running. Find a search keeps the jobs whose name, or set, holds your words, and the status choice keeps those waiting or running, done, or failed or stopped.

Query type

The page reads the query's type as you paste. Letters read as DNA or RNA when every one is a nucleotide code and at least 90% are A, C, G, T, U or N; anything else reads as protein. The line beside the chips says where the type came from. A click on a chip sets the type until you empty the box.

• A short protein made only of A, C, G and T reads as DNA. Choose Protein.
• A PIR record's header gives its type, and the line beside the chips says so. A chip that says otherwise is refused under the box.
• RNA reads as DNA / RNA, and its U is searched as T.
• A query that holds both DNA and protein records is refused under the box. Search one kind at a time.
• For a pattern search, the query type stays as you chose it.

A fault in the query shows under the box, names the line and the character, and selects it in the box. The message in the corner is for faults of the service.

Drop a file

Drop a file on the search card, or choose Open a file, and it goes where it belongs:

• A FASTA or PIR file fills the query box.
• A sequence listing, in WIPO ST.26 XML or ST.25 text, is imported under Sequence tools and opens its SEQ ID NO picker.
• A publication's full-text XML with claims offers Start a case from the publication's number. The case takes its claims, and its listing too when the file holds one. When the listing was filed as a file of its own, the offer says so; import it under Sequence tools.

While a search runs

The status bar under the search card follows your search. The tab's title reads "Running:" and the search's name until it finishes, then "Done:" until its result opens. A finished search opens its result by itself, unless you opened another result since it started or you are typing in a field; then it waits behind Open results. After a reload, the status bar follows your newest search that is waiting or running.

A running search says how long it has left, in whole minutes, from the server's estimate. A Smith-Waterman or global search of a DNA set also counts its queries as they finish, as in "2 of 5 queries done, about 6 minutes left", and works out the time left from their pace. When a search runs past that time, the line leaves the time out.

Addresses

An open result has an address of its own: /?job=<id> for a search and /?group=<id> for a combined search. A case at one of its steps has /?case=<id>&step=<step>. Back closes a result, and Copy link, in the result's header, copies its address. An address opens only for the account that ran the search; for anyone else, and for a search no longer on the server, the page says "This search is no longer on the server." The links in alert emails open the same way.

No match

A result with no match says so over its list and offers next steps. Each is a button that fills the search form, and you choose Run search:

• After BLAST of a short query (DNA under 50 bases, protein of 30 letters or fewer): Exact text, and Smith-Waterman for protein where FASTA36 is installed, on the same sets. Both read every stored sequence.
• After a search of the patent sets: the public sets of the same type, by the same method.
• After a protein search that read no DNA set: the DNA sets, translated.

Suggested searches

On a server with a snapshot of the patent sets, Suggested searches, over the search card, offers real public sequences to try, each linked to the record it comes from: the GLP-1 peptide against Patent proteins, the coding sequence of human insulin against Patent DNA, green fluorescent protein against Patent DNA read as protein, the antibody trastuzumab by its six CDRs (where antibody numbering runs), and the peptide SIINFEKL as exact text. 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.

Run fills the form as you would and starts the search, named "Suggested:" and the card's name. When it finishes, its result opens, unless you have opened another result or are typing in a field. Edit first fills the form and leaves the search to you. The result of a suggested search shows Things to try over its list: two or three steps that use it. Close hides them for that search in this browser. A suggested search is an ordinary search and stays in Recent jobs.

A sample result

A sample result is a search of a real public sequence, saved and shown read-only, so you can see what Sequences finds before you sign in. When a server has one, its sign-in page says "Not ready to sign in? See a sample result." and the samples are at /samples. A sample lists its patents as the Patents tab does: by family or by publication, sorted by Query Match, identity, date or sequences found. Set Published before to fold the later publications, as in Dates. Each row opens to its best alignment and, in a family, its members. A sample cannot be marked or run again: sign in to run your own searches.

Sets

A snapshot is a read-only copy of public sequence files, built on a known date. Each sequence in it is stored once and linked to every record and publication that holds it. A set, such as Patent DNA, is one collection in a snapshot. The page lists each set from the newest snapshot that holds it, with how many sequences it holds.

• A new search starts with every set of its type checked that the page may choose for you: Patent proteins and Swiss-Prot for a protein, Patent DNA and ESTs for DNA. Uncheck the ones you do not want.
• The page never selects TrEMBL for you. When you choose it, a line under the sets says how long the search should take, such as "TrEMBL is large: this search should take about 5 minutes."
• The hosted service also offers NCBI core_nt, a large DNA database outside the snapshot, which the page never selects for you either. It runs BLAST only, so the choice of method does not show for it.
• The patent sets hold US published applications, from the first, published 15 March 2001, and the US patents granted since 2001, from the US patent office's weekly full-text files and the sequence listings it publishes. An application and the patent granted from it share one sequence line when their letters match, so one hit lists both. Each week's applications and grants arrive as an addition: see Collection below.
• Sources and terms, below the sets, names the source and release of each set, its terms and its notices. Where the server has them, it also names the sources of paper citations and marks and of applicant suggestions.

A snapshot can get additions: newer records added after it was built. When a set's snapshot has them, choose under Collection: Main, the snapshot as built, which is chosen first, or Main plus New, the snapshot with every addition.

Only the local workbench can import a FASTA or PIR collection of your own, under Import a database: a file of up to 20 MiB and 100,000 sequences. A search of it runs BLAST, with up to 500 hits for each query (100 unless you change it under Search settings). The hosted service and other servers with sign-in do not take imports.

Search several sets at once

Check two or more sets under Search in to run one combined search: up to 8 sets, under one name, with one status bar and one result. A collection you imported is searched on its own.

• Translated search lists the sets of the other type than the query. There a protein query runs tblastn on a DNA set, reading each DNA sequence in all six frames, and a DNA query runs blastx on a protein set. These sets start unchecked. Exact text, Pattern, Smith-Waterman and the global methods compare like with like, so they leave these sets out.
• The status bar names each set as it goes, such as "Patent proteins done. Swiss-Prot running, about 2 minutes." Open results so far opens what has finished. A set still searching adds its references to the list when it finishes, and the row you selected stays selected.
• The result opens on References, one list for every set. A row is a patent publication or family, or a database entry such as a Swiss-Prot accession. It shows the best Query Match and identity across the sets and queries, the earliest date, and a chip under Found in for each set that found it. A patent that Patent proteins found, and Patent DNA found translated, is one row with both chips.
• Sort, Group, the date fold, the filters and the review desk work as in By patent. The Found in filter keeps what one set found, and Kind keeps patents or database entries.
• The pane lists the reference's matches by set and query, best first, under the best match's alignment. Choose another match to see its alignment.
• Keep and Exclude mark the reference in each search that found it, so the mark shows in each set's own result too.
• Applicants shows when the combined search holds one patent search. Search record lists each set's search with the SHA-256 of its own record and a button that opens that search by itself.
• Export matches (CSV) saves one line per reference that passes the filters, with the sets that found it. Download search record saves the combined search: its sets, each set's search and the SHA-256 of its record.
• If a set fails, the line over the list names it, with a button that runs that set again inside the same combined search. Run again runs every set again as a new combined search.
• Watch this search stays on each set's own search. Recent jobs shows a combined search as one card that names its sets.

Search methods

A search of a set in the snapshot offers these methods. A database outside the snapshot, such as core_nt, runs BLAST.

The three FASTA36 methods show only where FASTA36 is installed. The Sequences container image, which the hosted service and the server edition run, includes it. These methods return up to 5,000 sequences for each query, each with its best alignment. On DNA they search both strands, and a sequence can return once for each strand.

On DNA, Smith-Waterman finds short matches that BLAST misses. In our benchmark on Patent DNA, run when it held 28.8 million sequences, Smith-Waterman found 16 of 20 DNA fragments of 21 to 50 bases at 80% identity, where BLAST found 8. Each query reads every stored sequence, so a DNA search takes minutes, and longer on a larger set. In the benchmark, a Smith-Waterman query took about a minute at 21 bases and 5 minutes at 308 bases, global on the query took about 70 seconds up to 60 bases and 4 minutes at 308, and global on both sequences took about 25 seconds at any length. Patent DNA now holds 74.9 million sequences, with US published applications, and on the hosted service in November 2026 a Smith-Waterman query of 21 bases took 54 seconds. 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.

BLAST keeps hits with an E-value up to 10, or up to 1,000 for short queries: DNA under 50 bases and protein of 30 residues or fewer, which also run BLAST's short-query settings. The FASTA36 methods keep hits up to 1,000 for protein of 100 residues or fewer and for DNA under 50 bases, and up to 10 above that. Search settings has a Maximum E-value and a Maximum hits per query, and a value you set there applies to every query of the search.

FASTA36 fits its E-values to a random sample of scores, so a sequence near the cutoff can come and go between two runs of the same Smith-Waterman or global search. BLAST, exact and pattern searches return the same hits each time.

The automatic choice

Automatic is the first method on the list, and the search record says what it ran.

• Protein to protein runs Smith-Waterman. Where FASTA36 is not installed, it runs BLAST, and the search says "FASTA36 is not available here, so this protein search used BLAST."
• DNA to DNA runs BLAST. A query under 50 bases also gets an exact scan of every stored sequence on both strands, and the two are merged, so its exact matches lead the list and are complete.
• DNA to protein runs BLAST, and a query under 50 bases gets a warning: "A DNA query under 50 bases is short for a protein search, so a match can be missed."
• Protein to DNA runs BLAST.

Exact and pattern search

Exact text and Pattern read every stored sequence, so their counts are complete. They compare DNA with DNA or protein with protein. A DNA search covers both strands unless you clear Search both strands.

A pattern is parts joined by hyphens:

For example, AAGCTT-x(2,6)-GGATCC finds a HindIII site, 2 to 6 letters, then a BamHI site. In DNA, IUPAC codes such as R and N stand for their bases. A pattern takes at most 100 parts, 4 ranges such as x(2,6), repeat counts up to 1,000, and 20,000 characters.

A letter in a stored sequence matches only that letter, so an N in a stored sequence is not a wildcard. Each row is one sequence on one strand. Occurrences counts every place the text or pattern fits, and First positions lists up to 20 of them, counted from the start of the stored sequence. The list stops at 1,000,000 rows, and the totals still count every match.

Results

A finished search opens its results, 50 rows to a page, in tabs. Which tabs show depends on the search:

• Patents: one row for each patent publication that holds a matching sequence, in a search of the snapshot.
• Applicants: one row for each first-named applicant of those publications. It shows with Patents.
• Alignments: one row for each alignment, in every search. An exact or pattern search calls it Matches.
• CDR matches: the results of an antibody search, in place of Patents and Applicants.
• Search record: what the search used and returned: the search engine version, the set and snapshot it searched, every setting, and the SHA-256 of each file the search wrote. A SHA-256 is a fingerprint of a file: it changes if the file changes at all.

A search opens on Patents when it found a patent publication. One that found none, such as a search of Swiss-Prot, opens on Alignments, with the Patents tab beside it. An antibody search opens on CDR matches.

Each row of Patents and Alignments 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; on a narrower screen the pane opens under the row. The pane holds the row's measures, its marks and its alignment. These keys work while the list has the focus, and Keys, above the list, lists them too:

• Up and Down move through the list. At the end of a page they open the next or previous page.
• Page Up and Page Down move 10 rows. Home and End go to the first or last row.
• K keeps and X excludes the selected row, and the next row is selected. U clears its mark.
• R goes to the reason field, and Esc comes back to the list.
• C copies the alignment.

The line under the search's name says what it searched and the date of that set's source. Results for each query, above the tabs, gives each query's length, program, E-value cutoff and number of sequences returned. A query that reached its limit says so. A BLAST query's line reads "This query reached the 5,000-sequence limit. More matches exist." A FASTA36 search (ssearch36, ggsearch36 or glsearch36) keeps the best-scoring sequences at its limit, and its line reads "This query reached the 5,000-sequence limit. The list holds the best-scoring 5,000. For every exact occurrence, run the query as Exact text."

The results use four measures. Translated searches (blastx and tblastn) have no Query Match.

By patent

Group, above the list, sets what a row of the Patents tab is. With Families, the first choice, each row is one patent family: the publications that share a priority claim or an application, or, where no priority claim is on record, the same title and first applicant. The row shows the family's earliest publication, with its number, title and applicant and when it was published, the family's best Query Match and Identity, and how many sequences match, each counted once. A chip such as "+2 in family" counts its other publications, and the line over the list counts both, such as "12 publications in 5 families match these filters." A family of one publication reads as that publication. With Every publication, each row is one publication.

A publication's pane links its number to its page (Google Patents unless your server sets another address). Where a publication's record gives its filing date or priority claims, as a US published application's does, the pane shows them beside the publication date, such as "Filed 2026-06-09" and "Priority 2024-01-31". Many records in the patent sets give neither. The pane lists the publication's matching sequences by SEQ ID NO, with the best match's alignment under them; choose another to see its alignment.

A family's pane says how the family was formed: "Grouped by a shared priority claim," with the claim's number, "Grouped as publications of one application," with the application's number, or "Grouped by the same title and applicant. No priority claim is on record." It lists the family's publications, earliest first, each with its dates and an Open link to its page. It lists up to 20 and counts the rest; Every publication shows each one. Under them are the earliest publication's matching sequences, with the best match's alignment; choose another publication to see its own.

Rows that tie on the sort go earliest first, undated last, so among the rows with the best Query Match the earliest is on top. Published before tests each sequence by its earliest date and by the filing and priority dates of its US and WO publications, and folds the later publications under the list (see Dates). Applicants and a case's report count publications, whatever Group says.

By applicant

On the Applicants tab, each row is one applicant, the first applicant each publication names, with its publications, its earliest date and its best Identity. Rows are sorted by best Identity, highest first, then by earliest date, earliest first. An exact or pattern search has no identity, so its rows are sorted by earliest date. Publications that name no applicant come last, under "Applicant not given". The filters work as on Patents.

• Spellings that differ only in case, accents, punctuation or a legal ending such as Inc or GmbH share a row, and the row lists the other spellings.
• To treat names that still differ as one, such as a company's old and new names, select their rows and choose Join selected names. A join takes 2 to 50 names and covers all of your searches until you choose Undo join on its row.
• Join log, under the table, lists the joins and undos on your account, newest first: the newest 50, with the total when there are more. The log keeps every one. Each event holds the SHA-256 of the one before it, and Check the log reads every event to show whether any was changed or removed.
• Where an applicant's name matches an organization's name in the Research Organization Registry (ROR), the row links to that record under Suggested ROR record. A suggestion never joins or renames names. A server shows suggestions only when its staff have set them up.
• In a search of the snapshot, each row with an applicant's name has Watch this applicant and Export portfolio. See Watches and Portfolio export.

By alignment

Each row is one alignment of a query with a stored sequence: the hit, its title, and how many other publications hold the same sequence, such as "+4". A search of more than one query adds a Query column. A patent hit's title names the sequence's earliest publication. First published gives the hit's earliest date, or "Undated".

The pane gives the hit's measures and the alignment itself, 60 letters to a line, with each letter of the hit that differs from the query in bold. Copy alignment and Download .txt give the alignment as text. A patent hit's pane gives the earliest publication's applicant, with its filing date and earliest priority claim where its record gives them, and lists where the sequence is published: the earliest five, then Show all for the rest, 50 at a time. Then come up to five database entries that hold the sequence, linked to their records, and up to three papers, earliest first. See Papers. On a server that runs clinical context, a protein hit's pane can also have a Clinical context part. See Clinical context. On a server that runs the funding trail, a paper with grants in PubMed has a Funding part under it, and a hit can show its US published applications' statements on federally sponsored research after its papers. See Funding trail.

Papers

Where the server has PubMed's records, as the hosted service does:

• Each paper reads as a citation: up to three authors, the title, the journal, the year with volume, issue and pages, and the day it went online if that came before its issue. Its PubMed ID and DOI follow, each linked.
• A paper that was retracted, drew an expression of concern or was reinstated says so in a line 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 line says "notice date not given". Corrections are not marked, and a mark never moves or hides a paper.
• A PubMed ID that the National Library of Medicine deleted keeps its year, and a line says the paper is not in PubMed.

Without PubMed's records, a paper shows its title and year, linked to PubMed, or to its DOI when it has no PubMed ID, and carries no marks. A search keeps its papers as they were when it ran. To see newer citations and marks, use Run again.

Clinical context

Clinical context is an add-on: it shows only on servers whose staff have turned it on, as the installation guide's Clinical context section describes. Where it runs, a Swiss-Prot or TrEMBL hit whose UniProt entry is a drug target has a closed Clinical context part in its pane on Alignments, with the target's name and how many drugs act on it. Opened, it shows:

• The drugs that act on the target, highest clinical stage first, each with its mechanism and action.
• The diseases each drug is studied for, each with the highest stage it reached.
• Each disease's trials, ten at a time, with their phase and whether results were posted.

The target, drugs and diseases link to Open Targets, each drug to ChEMBL too, and each trial to ClinicalTrials.gov. The data come from Open Targets (with ChEMBL), ClinicalTrials.gov and AACT's copy of trial results, and Sources and terms credits them. The part names its sources and their dates, and it reports what they say without drawing a conclusion. Patent, EST and attached database hits show none, and neither does an antibody CDR search.

Funding trail

The funding trail lists the grants PubMed gives for each paper under a hit, with the NIH awards they match. It also shows the statements on federally sponsored research in the US published applications that hold a hit's sequence. It is an add-on: it shows only on servers whose staff have turned it on, as the installation guide's Funding trail section describes, and such a server has a funding trail card under Sources and terms.

PubMed lists each grant by its number. A grant shows as an NIH award when its number matches exactly one NIH project in NIH RePORTER, NIH's public database of research projects. An award here is one project under one project number. NIH funds a project year by year, so an award can span many fiscal years, each running from October to September.

On Alignments, a paper in a hit's pane has a closed Funding part when PubMed lists grants for it. Its label gives the counts, such as "Funding: 6 NIH awards, 1 other grant". Opened, it shows:

• The NIH awards, in the order PubMed lists their grants. Each has its project number, linked to NIH RePORTER, the title and each institution with its fiscal years. Then come the investigators NIH lists for the latest fiscal year that has any, with their names as NIH writes them. The contact investigator comes first, and in many older records the name ends in "(contact)".
• The other grants, as PubMed lists them, each with its number, funder and country.

Each list shows five, and the rest open under "N more". An award with many investigators shows six names and says how many more there are.

PubMed often lists one project in two ways, such as P30 CA016672 and P30-CA16672, and the award then shows once. All other grants show as PubMed gives them: grants from other funders, contracts, grants with no number, and numbers that match no single NIH project, such as an NIH grant older than the fiscal years NIH RePORTER covers. A number written with other words, such as ARRA R01HD065288, shows that way too, even when its project is among the awards. The part's first line gives the date of each source and the fiscal years NIH RePORTER covers.

The part shows what PubMed and NIH RePORTER list, and no award amounts. It does not show that a grant paid for the sequence, the work in the paper or a patent. The investigators are the people NIH lists for the award, not the paper's authors. A paper with no Funding part is one for which this server's copy of PubMed lists no grant, which does not mean the work had no funding.

A US published application whose invention was made with federal funding says so in its description. Where the server's funding trail holds these statements, a hit's papers are followed by a line, "Federally sponsored research, as the applications state it" ("as the application states it" for one), and a closed part for each application, named by its number and publication date. A hit shows up to three, from the earliest applications that hold its sequence. When more of them give a statement, a last line says how many, such as "2 more applications". Opened, a part shows the statement word for word, after the heading the application puts above it, if there is one. A statement that only says it does not apply, such as "Not applicable", is left out.

The statement is the application's own words, not matched to an NIH award or to a paper's grants. A hit without such a part may still come from federally funded work: its applications may not say so, or this server's copy may not hold the week they were published.

Keep and exclude

Each row of Patents and Alignments can be marked Keep or Exclude in its pane, and Clear takes the mark off. The keys K, X and U do the same from the list, and after K or X the next row is selected. A search of a collection you imported has no marks. Type a reason in Reason (optional) before you mark the row, and it stays with the mark. To give a marked row a new reason, type it and press Enter. The list's Mark column says "Kept" or "Excluded". Excluded rows leave the list until you choose Show excluded. The CSV files keep every row that passes the filters, excluded ones too, with the marks and reasons. A result opened from a case records each mark in the case's log, and the case's report lists the publications and matches you keep.

On Patents with Families, a mark on a family row goes on each of its publications in the list at once, but not on later ones the date folds, and a case's log records it as one event that names them all. The Mark column says "Kept" when every publication of the family is kept and "Some kept" when only some are; the pane says how many, such as "2 of 3 kept." To mark one publication of a family, choose Every publication. A publication you exclude leaves its family, and Show excluded lists it.

Align exactly

After a BLAST search of a set in the snapshot that compares like with like (blastn or blastp), and where FASTA36 is installed, each row has a Select box. Select up to 1,000 rows, or choose Select this page, pick Smith-Waterman (local) or Global on the query under Exact alignment, and choose Align exactly. The whole query of each selected row is aligned again with the stored sequence, and the new scores join the row and the CSV. Global on the query aligns every letter of the query, so its scores cover the query's full length.

Dates

Each sequence is dated by the earliest date known for it, across its patent publications, its database entries and its papers.

• A patent publication is dated by its publication date, not by its filing or priority date, even where its row shows them.
• With Published before set, a sequence first published on or after your date still passes when one of its US or WO publications was filed, or claims priority, before your date, where the record gives those dates, since such a publication can count as prior art from that earlier date.
• A UniProt entry is dated by the day its current sequence version appeared.
• An ENA record at version 1 is dated by the day it first appeared in ENA. A later version has no date of its own, because ENA does not say when its sequence changed.
• A paper is dated by the day PubMed gives for it: the earlier of the day it went online and its issue date. A paper that PubMed dates only by month or by year counts as dated before the first day of that month or year. So with Published before June 15, 2015, a paper dated only June 2015, or only 2015, still passes.
• Without PubMed's records on the server, a paper is dated by its year only, in the same way.
• A core_nt hit that ENA also holds shows ENA's description and papers. At version 1 it is dated by the day it first appeared in ENA, or by an earlier paper where the server has PubMed's records. Other core_nt hits are undated, and their papers do not date them.
• A sequence with no known date reads "Undated" and always passes the date filter.

On Patents, with Published before set, the list holds the publications from before your date, the US and WO publications published after it but filed or claiming priority before it, marked "Filed before" ("Filed before your date" in the pane), and the undated ones. The later publications of the same sequences fold under the list, in one line such as "3 later publications of these sequences are folded. 1 of them is a US or WO publication with no filing date on record." Such a publication may still have been filed before your date, so check its page. Show them brings the folded publications back, each marked "After date" ("Published on or after your date" in the pane), and Fold them again folds them. A family keeps its publications from before your date in the list, and its pane counts the ones folded. Without a date nothing folds, and a new date folds them again.

Filters and sorting

The filters change the list, and the CSV export follows them.

Sort patents orders the rows of Patents, families or publications, by the highest Query Match or identity, the earliest or latest date, or the most sequences. Rows that tie go earliest first, undated last, and rows of one date go highest Query Match first. Sort matches orders alignments by bit score, E-value, Query Match, identity, query identity or query coverage, and alignments that tie go by their sequence's first published date, oldest first.

Exports and search records

• Export matches (CSV) saves the rows of the tab you are looking at that pass its filters, with their marks. On Patents it saves one row for each publication, whatever Group says, the folded later publications too, with application_number, filed and priority, then its patent family and its place against your date. A family is the publications that share a priority claim or an application, or, where no priority claim is on record, the same title and first applicant: family names its earliest publication, family_size counts its publications, and family_basis says how they were joined (priority, application, title, or single for a publication on its own). date_group is before, filedBefore (published on or after your date, but filed or claiming priority before it), later or undated, and empty without a date. On Applicants it saves one row for each applicant, with its other spellings, publications, joins and ROR suggestions. On Alignments it saves one row for each alignment, with the columns entries, papers, pubmed_ids, dois, paper_dates and paper_marks, and then the earliest publication of the hit's sequence, the one its title names: first_publication, first_kind, first_applicant, first_filed, first_application_number and first_priority. The filing and priority columns are filled only where a record gives them, as on Patents. A priority cell lists every claim, earliest first. On CDR matches it saves the table on the screen.
• Download search record saves the search's record as JSON: the search engine version and each search program's version, the set, snapshot and additions it searched, every setting, each query, the PubMed data its papers came from, if any, and the SHA-256 of each file the search wrote. The engine version is the Search engine number of the release notes. For a search of a collection you imported, the button reads Download full search record, and the file holds every hit as well.
• The Search record tab shows the main parts of the same record on the page.
• Export portfolio, on a row of Applicants, saves one applicant's publications with their sequences. See Portfolio export.

The results page and the search record state the search's limits, such as how many sequences each query returns, and end with "These results do not establish patentability."

Run again

Run again starts a new search with the same request as a finished one: the same queries, settings, snapshot and additions. It finds an older snapshot by its ID while that snapshot is still on the server. Once the snapshot is gone, it answers "Snapshot not found." An antibody search runs again on the CDRs it found, without numbering the chains again. A search that a case's plan started has no Run again: open the case and run its plan again.

Watches

A watch follows a finished search of the snapshot, or an applicant, through each addition of newer records to the snapshot. It shows only what is new: matches the search has not found before, or the applicant's new publications.

1. To watch a search, open a finished search of the snapshot and choose Watch this search. The button then reads Watching.
2. To watch an applicant, choose Watch this applicant on its row under Applicants, or write its name under Watch an applicant in Your watches, below Recent jobs on the search page, and choose Watch. The form watches the applicant in the newest snapshot that has patent sets. Case, accents, punctuation and endings such as Inc do not matter, and the names you have joined to it count too. The form does not look the name up, so a watch on a name that no publication names first lists nothing until a new publication does. A watched row reads Watching, which goes to the watch.
3. Your watches lists each watch with its state: Watching, Running, Paused or Needs attention. A watch on a search opens its results. A watch on an applicant names the applicant and how many names are joined to it, and has Export portfolio. Each watch can be paused, resumed or deleted.
4. The server looks for additions every hour, so a watch runs within about an hour after one arrives. A run that fails is tried up to 3 times.

• A watch on an applicant runs no search. After each addition it lists the applicant's new publications, each with its date and number of sequences, linked to the patent.
• As under Applicants, a publication counts for the first applicant it names. A watch on an applicant finds only what the patent sets hold, US published applications among them. See Sets.
• Needs attention means the watch has a problem or its last run did not finish. The line under it says why, and whether the watch tries again within the hour or waits for the next addition.
• An account may have 50 watches, of searches and applicants together.
• A watched search may hold up to 50,000 matched records. A watch whose results grow past that pauses, and says so.
• Antibody searches cannot be watched.
• The line under Your watches says whether this server emails what your watches find. The hosted service sends no watch emails, so what its watches find shows under Your watches only, as on any server without them. Where a server sends them, each email goes to your address and has a link that pauses the watch without signing in.

Portfolio export

A portfolio export saves one applicant's publications with their sequences, as a CSV file and a FASTA file.

1. Choose Export portfolio on the applicant's row under Applicants, or on its watch. The export runs as a job in Recent jobs.
2. It collects every publication in the snapshot and its additions whose first-named applicant is this one or a name you have joined to it, with each of their sequences in Patent DNA and Patent proteins.
3. When it finishes, Download CSV and Download FASTA save its files, on the applicant's row under Applicants and on the export's card in Recent jobs. The row and the card say what the export holds, such as "The export holds all 2 sequences, from 1 publication." On the row, Export again starts a new export, for example after a new join.

• The CSV has one row for each sequence, with the columns publication, published, applicant, seq_id_no, accession, molecule_type, length and sequence. The FASTA file holds the same sequences.
• An export holds up to 100,000 sequences and 100 million letters. It takes the oldest publications first, and each publication's sequences by SEQ ID NO, so an export that stops at a limit leaves out the newest publications. Its line then says how many of the applicant's sequences it holds, from how many of the oldest publications.

Cases: claims to search plan

A case turns claims into a search plan that you review and lock before any of its searches run, and it keeps a log of every step. Start one under Claims to search plan with a Case name and, if you have them, the Sequence listing that holds the sequences the claims recite by SEQ ID NO and the Snapshot to search. First import the listing under Sequence tools. You can choose it here, or later in the Plan step.

You can also give the Application number and the Prior art date. New searches look for what was published before the prior art date. Leave the date empty and a publication XML file gives its filing date. The case header shows both, such as "Prior art date 2020-03-02 (filing date)". Choose Change to edit them. A locked plan version keeps the dates it was locked with.

1. Claims: choose Paste the claims, Publication XML file for one publication from the US patent office's full-text files, an application or a grant, up to 20 MiB, or Word or text file for claims in a .docx or text file of up to 15 MiB. A publication's number and dates come with its claims. A weekly full-text file holds many publications one after another, so save the one you need as a file of its own. When the file gives an earliest priority date too, the step offers Filing date, Earliest priority date or Another date as the prior art date. Use this date saves your choice. A case can hold the claims as filed, as amended, as published and as granted: see Sets of claims. Under What the description says about each claimed SEQ ID NO, the step gives a summary of each SEQ ID NO the claims recite. See Summaries.
2. Review: the case reads each claim and marks what it recites: SEQ ID NOs, identity thresholds, fragments, complements, fusions, regions, CDRs, sequences written out in the claim, the changes a claim allows, such as "one, two or three amino acid substitutions", and letters a claim reads as any residue, such as "wherein X is any amino acid". Accept, reject or edit each finding, or select words in a claim to add one. Where the server offers suggestions from a language model, the step names the model, and a button marked "(Pilot)" asks it for missed features. It sends the claims and, for claims from a publication XML file, up to 40 paragraphs of the description that cite a SEQ ID NO the claims name or define a term they use. A model can take minutes: the step shows how long it has been asking, and you can keep working. The server asks for one case at a time; while the model answers for another case, the step says to ask again in a few minutes. Each suggestion names the model, and its threshold, range or length counts only when the claim's own words state each number. A suggestion may quote the paragraph of the description it draws on. None counts until you accept it. Otherwise the step says "Model suggestions are off."
3. Plan: the searches your accepted findings call for. A draft searches each set on the server that holds the finding's type, patent sets first: for a protein, the patent proteins and Swiss-Prot. It searches each SEQ ID NO once, at the lowest identity any claim gives it. A search's identity counts a letter that stands for more than one residue, such as X for any amino acid, as a difference, while References reads it as each residue it stands for. So where a SEQ ID NO holds such letters, its search 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 its 15 letters, X and Z, as differences." A claim that allows changes, such as "with one, two or three amino acid substitutions", is met by a match with that many of those changes or fewer, so its search keeps the identity that many changes of any kind leave, and its reason says so, such as "Keeps 80% identity or more, which 3 changes leave in its 15 letters." References then reads which matches meet the claim. Set to search lists every set of the search's type, from any snapshot on the server, and each attached database. TrEMBL, and an attached database such as core_nt, take much longer, so they join only when you ask: a button such as Add TrEMBL adds a copy of each fitting search and says how long they should take. Lock as version 1 records the plan and its SHA-256, and only a locked version runs. To change a locked plan, choose Unlock the plan. The next lock makes version 2.
4. Run: pick a locked version. The case checks that it has not changed since you locked it, then runs it. A large plan, such as one search of 250 SEQ ID NOs, needs more jobs than the queue holds. The case starts what the queue has room for and starts the rest as jobs finish. It always leaves 2 places for searches from the form. Each run shows a line such as "7 of 12 searches done, about 4 minutes left". When the server restarts, the run goes on by itself. A search that failed has Run this one again. The results open with the plan's filters.
5. References: every reference the case's searches found, under the claim feature whose search found it, ranked by fixed rules, with summaries of the references and the searches. See The References step and Summaries.
6. Report: the case's application number and prior art date, the plan's searches, up to 100 other searches that you add under Add a finished search or bring in under Import a result file (see Result files from other programs), the notes you add under Notes (up to 500 in a case, each up to 5,000 characters), the sentences under Why each reference counts and the summaries you accept or edit. Download PDF and Download Word save the report. For each search it gives the settings, the publications and matches you kept, with each kept match's papers and alignment, its top 15 publications by best Query Match and its top 25 matches. Its publication tables add a Filed column when a publication's record gives its filing date or priority. By applicant, after the table of searches, groups the publications you kept, and the publications that hold each match you kept, by applicant across all of the case's searches, with your joins: up to 100 applicants, each with up to 20 publications, and it says how many more there are. A table lists the searches of the latest locked plan version, with each one's query, method, set, thresholds and reason, and then the features no search covered. The server keeps no copy, and the log records each report's SHA-256. Download decisions (CSV) and Download decisions (JSON) save every decision in the case. See The decisions file.
7. Log: every step in the case. Each event holds the SHA-256 of the event before it, so a changed or deleted event shows. Verify the log checks this.

Sets of claims

A case can hold an application's claims as filed, as amended on a date, as published and as granted. Each import is a set of its own, and the case keeps every set with its source, date, SHA-256 and who added it.

• These claims are says what the claims are: As filed, As amended, As published or As granted. A publication's XML says it for you: an application's claims as published and a patent's as granted, each with the publication's date. Claims as amended need their Date of the claims.
• A Word file marked up as an amendment reads as the claims as amended: struck-through and deleted text is left out, and underlined and inserted text is kept. In a claim marked "(Currently amended)", text in double brackets, such as [[about]], is left out too. Pasted text loses strike-through, so for an amendment send the Word file. An older Word file (.doc), a Word file saved with a password, or a PDF cannot be read: save it as .docx, or paste the claims.
• A new set becomes the current set, unless it is dated before the current set. Then it is kept beside it, and Make current, under Sets of claims, makes it current, with an optional note for the log.
• When the current set changes, the rules find its features again. Each decision you made carries over wherever a claim's words did not change, even when the claim was renumbered. No model is asked again. An unlocked plan loses its searches.
• A locked plan stays locked and follows the set it was locked on, and its searches run on those claims. To search the current set, unlock the plan with a reason, which the log keeps, and draft it again. The report names the set the plan follows, with its label, date, source and SHA-256.
• What changed compares any two sets claim by claim. Each claim is unchanged, amended, added or cancelled, and a renumbered claim shows its number in both sets. In an amended claim, added words are underlined and removed words are struck through.

The References step

References lists every publication and database entry the case's searches found, under the claim feature whose search found it. A feature is a SEQ ID NO you kept in Review, with the identity, fragment length and allowed changes that apply to it, or a sequence written out in a claim. Each feature shows the claim's words, such as "at least 90% identical to SEQ ID NO: 1", its threshold and the searches that serve it.

• A search the plan ran serves the features its plan search covers, and keeps the filters it was locked with.
• A search you add in Report serves the features that recite its query's SEQ ID NO when it ran on the case's listing. The references of any other search are under Other searches, which has no threshold.

Inside a feature, the references rank by four rules in order. No language model takes part, so the same results always give the same order.

Ties go to the earliest publication, then the ID.

• Each row shows its rank and each score beside it: Meets, Coverage, Date, Query Match, E-value and the mark. A narrow screen leaves some of these columns out. Open the row to see them all. Meets reads "Meets", "Below" the claim's identity, "More changes" than the claim allows, "Other changes" than the kinds the claim allows, or "Differs" from a claim that reads as written.
• Click a row, or press Enter on its name, to open it. It gives the scores in words, such as "Meets 90%: 97.3% identity over the full query" or "Meets as written: 93.3% identity over the full query, and 1 position is X, read as any amino acid" or "Meets up to 3 substitutions: 1 substitution, 93.3% identity over the full query", and "Published 2011-09-22, before the prior art date", the search and row of the best match, and Open results, which opens that search's results. Escape closes the row, and the Up and Down arrow keys move between rows.
• Under a claim that allows changes, the words count the best match's changes of each kind. A match with a kind of change the claim does not allow reads, for example, "Changes other than substitutions: 2 deletions, 86.7% identity over the full query". Under a claim of conservative substitutions, the words say "2 substitutions, not checked as conservative".
• A percentage that misses a threshold is never rounded up to it: 89.96% shows as 89.96%, not 90.0%.
• For a feature with more than one SEQ ID NO, a row says how many it matches, such as "Matches 37 of 250 SEQ ID NOs".
• Each feature lists 20 references at first, and a button such as Show 20 more adds the next ones.
• Marks come from each search's results. The Mark column reads "Kept", "Excluded" or "Mixed", and the open row names each search's mark, such as "Kept in search 1, excluded in search 3". A reference that every search that found it excluded leaves the list. Show excluded lists those references.
• Download CSV saves every reference of every feature, with the claim's words, the scores and the best match. The excluded references come last in their feature, with no rank.
• Reading the list changes nothing in the case or its log.

Summaries

Sequences writes short summaries in a case from fixed templates and the case's own facts. No language model takes part, so the same facts always give the same words in the same order.

• There is a summary for each search that adds references, for each feature's first 5 references and the ones you keep, and for each claimed SEQ ID NO. Claims lists the first 10 SEQ ID NOs, and a button such as Show 10 more adds the next ones, up to 200.
• A search's summary describes what the search returned, before your marks, so keeping or excluding a reference never changes it. A line over the searches' summaries says so. Your marks show in the Mark column of the references above them, and in the report in each search's own section.
• A summary is filled in again from the case each time you open it, so it says what the case holds now. Each sentence names its source: a claim, a paragraph of the description, a search, a result row, a publication or the case. Sequences checks that every number, date, SEQ ID NO and publication number in a summary is one its facts hold, and that every quote is in the paragraph it names.
• Under each summary, "Filled in from template" names the template and the start of its SHA-256, so you can tell which wording filled it in. A change to a template's words gives it a new name.
• Choose Accept, Edit or Reject. An edit is one paragraph in your own words, and the summary keeps the draft beside them. A summary you neither accept nor edit stays out of the report. 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, for example when you change the prior art date, the summary asks you to decide again, and it leaves the report until you do. The summary of a reference that you exclude after deciding also leaves the report.
• Pasted claims come without a description, so each SEQ ID NO's summary names only the claims. Import the publication's XML file, and the summaries quote the paragraphs that cite each SEQ ID NO.
• The report prints the summaries you accepted or edited under Summaries, after By applicant, each with the template that filled it in and who accepted it, and when. The case log records every decision.

Why each reference counts

In the Report step, Why each reference counts lists each search in the case. For each publication you keep, and for the 5 publications of each search with the best Query Match, the case drafts up to four sentences from what it stored. Each sentence states one fact:

A sentence that has no fact to state is left out. Each sentence names its source, with a button or link to it: the result row, the plan version, or the publication's or paper's page. No language model writes the sentences, so the same facts always give the same words.

• The date is the case's prior art date. A case with none uses the filing date that came with a publication XML file, and for a search the plan ran, the search's Published before date. With no date, there is no date sentence.
• Choose Accept, Edit or Reject for each sentence. An edit keeps the draft beside your words. A sentence you neither accept nor edit stays out of the report.
• The report prints the accepted and edited sentences of the publications you keep, with their sources. Top publications you have not kept are listed in a collapsed section, such as "2 top publications not kept". What you accept there goes in the report once you keep the publication.
• When the facts behind a sentence change after you decide, for example when you reject a finding that the sentence names, the sentence says that its draft changed, and it leaves the report until you decide again.
• The case log records every decision.

Result files from other programs

You can run a search outside Sequences, such as BLAST+ or FASTA36 on your own computer against the patent sequences, and bring its results into a case. In the Report step, under Import a result file, choose the file and then Import the file. The import becomes one of the case's searches. It opens in the same results view as any search, with marks, families, dates and the sentences under Why each reference counts, and its references join those of the case's other searches in References.

Sequences reads these files, as they are or gzip compressed:

The names in a CSV header match in any case: qseqid or query, sseqid or subject, pident or identity, length, qstart, qend, sstart, send, evalue, bitscore or score, publication and seq_id_no. Each row needs a subject, or a publication and a SEQ ID NO.

• Each row joins a stored patent sequence of the case's snapshot and its weekly additions: by accession, such as AX123456.1 or gb|AX123456.1|, or by publication and SEQ ID NO. A publication number can be written as US20200012345A1 or US-2020-0012345-A1, or with spaces and a slash. A publication written without its kind code, such as A1 or B2, joins only when one kind holds that SEQ ID NO.
• A search of a Sequences snapshot's own files, such as a copy of the patent sets on your own computer, names each sequence by its place, such as cb26. Such a row joins when the file names the database by a path that includes the snapshot's folder and the case searches that snapshot. BLAST+ writes the database in -outfmt 5, 7 and 15, and FASTA36 in -m 8 with its comment lines. A plain tabular file names no database, so its places do not join, and the reason says so.
• A file that names its program joins the set that program searches, such as Patent DNA for blastn and Patent proteins for blastp. A CSV file, or a file that names no program, joins both. Look up its sequences in picks one set.
• A row that does not join stays in the results, with the reason as its title. Rows that did not join lists them with their reasons, and Download them as CSV saves them all.
• A row shows its alignment when the file has one. BLAST XML and JSON files have alignments, and tabular files have them when they include the qseq and sseq columns.
• On the command line, blastn runs megablast unless you add -task blastn. Megablast finds close matches and can miss weaker ones. Sequences runs blastn, so add -task blastn when a file should compare like for like with Sequences' own search.
• The case log records the import with the file's name, size, format and SHA-256. The report names the file and its SHA-256, how many rows joined, and the first rows that did not, each with its reason.
• An import counts as one of the 100 searches you can add to a case, and Remove takes it out again.

The decisions file

Under the report buttons, Download decisions (CSV) and Download decisions (JSON) save every decision in the case:

• Each claims import, with the rules version that read the claims and the set it became, with its label and date, and each change of the current set. Each row also names the set that is current now.
• Each claim feature as it stands: where it came from (the rules, a model or you), its rule, kind, claim, quote, details, links and status. The details of allowed changes name the kinds that count, such as "Up to 3 substitutions only".
• Each accept, reject and edit, and each feature you added, with who did it, when, and any note. An edit gives the quote, details and links before and after it.
• Each call to a claims model: the model, the prompt's ID and SHA-256, each suggestion kept, with what became of its details and its paragraph of the description, and each suggestion dropped, with the reason. A failed call gives its error.
• Each decision on a drafted sentence, with the last one on each sentence marked.
• Each decision on a summary, with the template that filled it in, the SHA-256 of the template's words and of the summary's facts, and the last one on each summary marked.
• The plan's locked versions, and each draft, edit, lock and unlock, with the reason given for an unlock.

Each decision gives the number and SHA-256 of its event in the case log, so you can check it against the log. The JSON file also gives the result of the log's check. Saving the files changes nothing in the case or its log. Only people who can open the case can download them.

Listings and the ST.26 check

The Listings tab of Sequence tools reads sequence listings and checks them before they are filed.

• Import a WIPO ST.26 XML or ST.25 listing, plain or gzip, of up to 256 MiB unless your server sets another size. A gzip file can unpack to at most four times that size. The page compresses a large file before it uploads it. Then pick up to 20 of its sequences, 100,000 letters in all, and choose Start the searches.
• Import a publication's full-text XML when its listing is inside it, as in the patent publications of 2001 to 2004. Sequences reads the listing inside. If an entry cannot be read, it is left out and the listing names it, such as "SEQ ID NO: 3 could not be read". A publication whose listing was filed separately says so: import that listing instead.
• Check a listing before you file it: choose a file to check against WIPO ST.26, version 1.7. The check runs in your browser, so the file does not leave your computer. Every problem names its SEQ ID NO and line. 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 choose Download problems (CSV).

Antibody CDR search

Turn on Antibody CDRs, beside the search card's title, to find the patents and stored sequences that hold an antibody's CDRs.

1. Under Search for, choose CDRs of antibody chains and paste up to 10 heavy or light chains of up to 2,000 letters each, then choose Number chains. Human and mouse heavy, kappa and lambda chains can be numbered. Or choose CDRs typed in and type H1 to L3, 1 to 80 letters each. Edit these CDRs changes what the numbering found.
2. Choose the numbering (Kabat, Chothia or IMGT), a protein set and a Minimum identity from 50 to 100 percent, 80 by default, then choose Search CDRs.
3. Each CDR runs the exact scan and, where FASTA36 is installed, Smith-Waterman, with up to 5,000 sequences for each CDR.

CDR matches groups the results by patent or by stored sequence, and Only those with every CDR keeps the rows that hold all of them. Each cell reads exact, the identity of the best alignment, or missing. A CDR counts as found at the minimum identity or more over its full length.

Sequence tools

Besides Listings, Sequence tools has three tabs:

• Editor: check, slice, reverse complement and translate a sequence, show its six frames, and Fetch a sequence from the snapshot by accession, or by publication and SEQ ID NO.
• Fragments: the sequences you saved, each with its edit history.
• Align: align two sequences by Smith-Waterman or global alignment, or many sequences, up to 200, with MAFFT and a majority consensus.

Who can see your work

• On the hosted service and on a server with sign-in, your searches, portfolio exports, cases, listings, saved sequences, watches and applicant joins belong to your account. No other account can open them.
• An admin's usage page counts each account's searches and other work. It shows counts, not content.
• An admin can also download a file of the decisions in every case, to measure how well the claim rules and model prompts work: each feature's kind, rule, source and status, each model call's counts and the reasons suggestions were dropped, in fixed words. The file holds no claim words, quotes, notes or edits, since claims pasted into a case can be from an application that is not yet published.
• The people who run a server hold its stored files: ConductScience for the hosted service, and your organization's staff for a server it runs.
• You can delete a listing, a saved sequence or a watch. Searches, portfolio exports and cases have no delete, on the page or through the API.
• On the local workbench there are no accounts: everyone who can open the page sees all the work saved there.
• Claim text leaves the server only when you ask for model suggestions, and then it goes to the model the server names, with the paragraphs of the description chosen for it. The case keeps a record of each call: what was sent, the model's answer, and each suggestion kept or dropped with the reason.
• Where a server emails what your watches find, each email goes through Resend, an email delivery service, and carries the watch's name and its new matches or publications to your address. The hosted service sends no watch emails.
• The ST.26 check runs in your browser and sends nothing.

Programs and API tokens

Programs can run searches through the same routes the page uses.

• On the hosted service, and on a server whose sign-in takes API tokens, open API tokens beside your account. Name the token and pick how long it lasts, up to 90 days (your server may set less). Copy it right away: the page shows it only once. An account may have 10 live tokens. The page shows when each token was last used, and Revoke ends one.
• The program sends the token with every request, as Authorization: Bearer <token>, and acts as your account under the same rules.
• GET /api/openapi.json describes the routes a program uses, in OpenAPI 3.1. It is open without sign-in.
• 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. An account may have 200 batch searches waiting or running.
• On a search's patents, GET /api/jobs/:id/publications takes group=family for one row per patent family, at its earliest publication, with its members and how they were joined, and later=hide to fold the publications from on or after the Published before date and count them. POST /api/jobs/:id/marks takes ids to keep or exclude up to 500 publications at once, such as a family's. The OpenAPI description gives every field.
• GET /api/jobs takes text to find your searches by name, or by the set or database they searched, and status to keep those in the states you list, such as queued,running. GET /api/jobs/:id/request gives the request a search was started with, query included.
• POST /api/groups runs one search across 2 to 8 sets as a combined search, such as a protein query against Patent proteins, Patent DNA and Swiss-Prot. If one set cannot take the query, or the queue lacks room, none starts. GET /api/groups/:id/references gives one list: a patent or database entry that several sets found is one row, with its best measures, its earliest date and the sets that found it. It takes the filters, sorts, group=family and later of a search's patents, plus set and kind. A mark through POST /api/groups/:id/marks reaches every search in the combined search. On the page, Search in starts one when you check two or more sets.
• GET /api/jobs/:id/hits/:row gives one hit of a search by its row number, whatever the filters, with its mark.
• POST /api/cases/:id/imports?name=<file name> brings a result file into a case, as Import a result file does. Send the file itself as the body, as application/octet-stream, or as application/gzip when it is compressed. GET /api/cases/:id/imports/:jobId/unresolved lists the rows that did not join, with their reasons.
• A token cannot make another token: that needs the browser. On the local workbench there are no tokens, and a program on the same computer calls http://127.0.0.1:8765 as the page does.

Data sources and dates

Each set is built from public files, and Sources and terms on the search page names the release, the terms and the notices of each one. The page lists each set from the newest snapshot that holds it. On the hosted service, the patent sets come from the snapshot of November 5, 2026, built from GenBank release 274.0 and the patent protein files of EMBL-EBI. Swiss-Prot, TrEMBL and the ESTs come from the snapshot of November 10, 2026; the ESTs are from ENA's files of September 10, 2026. NCBI core_nt is outside the snapshots, and a search of it names the date of its copy under the search's name. Paper citations, dates and marks come from PubMed records revised up to November 8, 2026 and the Retraction Watch Database of November 6, 2026, and the genes and diseases a paper names from PubTator 3 of October 6, 2026. Applicant suggestions come from ROR v2.15, data of October 20, 2026. A server your organization runs has the data its staff loaded, and Sources and terms names it.

Limits

BLAST can miss matches that an exact scan or Smith-Waterman finds. These results do not establish patentability. Questions about Sequences go to support@conductscience.com.