The Uniprot Free Text Search Interface

The Uniprot Free Text Search Interface

Jalview provides a specialised interface that allows fast and efficient discovery and retrieval of data from the Uniprot database. It allows interactive querying of Uniprot metadata with free text and structured queries, so sequences can be located without prior knowledge of their database accessions, or via manual cross-referencing from Uniprot or other bioinformatics websites.

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 2.9.1)

Searching the Uniprot Database

To search the Uniprot, begin typing in the text box. The results of your query are shown in the search results tab, which queries Uniprot after 1.5secs every time you type in the search text box. You can sort results according to 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 and visualise the sequences in Jalview Alignment interface.

Searching a specific Uniprot field If you want to find sequences based on a specific Uniprot metadata field, you can select it from the drop-down menu.
Bulk Uniprot retrieval
Firstly, switch the search target to Uniprot Id, then enter multiple IDs by separating them with a semi-colon. e.g. fila_human; mnt_human; mnt_mouse.
Hitting Return or OK will automatically fetch those IDs, like the default Sequence Fetcher interface.

Advanced / Custom querying The table below provides a brief overview of the supported Uniprot query syntax (see query fields for UniProtKB):

`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.
`citation:(author:Arai 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 displayed or remove.

The Uniprot Free Test Search Interface was introduced in Jalview 2.9.1