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.

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