The UniProt Free Text Search Interface

The UniProt Free Text Search Interface
Since version 2.10 (October 2016), the Jalview Desktop provides a search interface for interactive discovery and retrieval of sequence data from UniProt. This dialog enables UniProt sequence metadata to be searched with free text and structured queries, which allows sequences to be located via gene name, keywords, or even via manual cross-referencing from UniProt or other bioinformatics websites.

Please Note:UniProt updated their API in July 2022. Versions of Jalview older than 2.11.2.4 will not work with the July 2022 UniProt free text search.
The new UniProt API has a different search syntax for ranges of dates and numbers, and different query fields for advanced searches. The general syntax of combining queries remains the same. Because of these differences, your previously saved searches will not appear in the dropdown list next to the search box. If you need to access these old searches they can be found in your ~/.jalview_properties file with the label CACHE.UNIPROT_FTS. If you want to transfer them to the new API search then copy the values to the CACHE.UNIPROT_2022_FTS label (or rename the existing label if the new one does not exist) (see the UniProtKB query fields page).
A change in accepted formats for number and date ranges means that number ranges should now always be entered as e.g.[1 TO 100] or [2020-01-01 TO 2022-07-26] although a * wildcard can be used for half-open ranges, e.g.[2020-01-01 TO *]. See the UniProtKB query fields page for more examples.

To open the UniProt Sequence Fetcher, select UniProt as the database from any Sequence Fetcher dialog (opened via "File →Fetch Sequences").

UniProt sequence fetcher (introduced in Jalview 2.10)

Searching the UniProt Database

To search UniProt, simply begin typing in the text box. If the 'autosearch' check box is enabled, then after a short delay (about 1.5 seconds), results will be shown in the table below. Results are also updated whenever you press Enter, and you can access previous searches by pressing the 'Down' arrow or clicking the drop-down menu icon at the side of the search box.

You can sort results by clicking on the displayed columns, and select entries with the mouse or keyboard. Once you have selected one or more entries, hit the OK button to retrieve the sequences.

Searching a specific UniProt field To find sequences with particular UniProt metadata, you can select a field to search from the drop-down menu.
Bulk UniProt record retrieval
To retrieve sequences for a list of Uniprot accessions, please enter them via the 'Retrieve IDs' tab.

Complex queries with the UniProt query Syntax The text box also allows complex queries to be entered. The table below provides a brief overview of the supported syntax (see the UniProtKB query fields page for more details):

`human antigen`	All entries containing both terms.
`human AND antigen`
`human && antigen`
`"human antigen"`	All entries containing both terms in the exact order.
`human -antigen`	All entries containing the term `human` but not `antigen`.
`human NOT antigen`
`human ! antigen`
`human OR mouse`	All entries containing either term.
`human \|\| mouse`	All entries containing either term.
`antigen AND (human OR mouse)`	Using parentheses to override boolean precedence rules.
`anti*`	All entries containing terms starting with `anti`. Asterisks can also be used at the beginning and within terms. Note: Terms starting with an asterisk or a single letter followed by an asterisk can slow down queries considerably.
`author:Tiger*`	Citations that have an author whose name starts with `Tiger`. To search in a specific field of a dataset, you must prefix your search term with the field name and a colon. To discover what fields can be queried explicitly, observe the query hints that are shown after submitting a query or use the query builder (see below).
`length:[100 TO *]`	All entries with a sequence of at least 100 amino acids.
`(lit_author:Arai) AND (lit_author:Chung)`	All entries with a publication that was coauthored by two specific authors.

Result pagination

The query results returned from the UniProt server are paginated for performance optimisation. The button labelled ' << ' and ' >> ' can be used to navigate to the next or previous result page respectively. The page range is shown on the title bar of the Free Text Search interface. Jalview's pagination implementation supports multiple selection of entries across multiple pages.

Customising The UniProt Sequence Fetcher

To change the displayed meta-data in the search result, click the 'Customise Displayed Options' tab, and select the fields you'd like to be displayed or removed.

The UniProt Free Test Search Interface was introduced in Jalview 2.10.0 and updated to the July 2022 API in Jalview 2.11.2.4