From: Jim Procter Date: Mon, 5 Sep 2016 16:20:10 +0000 (+0100) Subject: JAL-1563 UniProt FTS doc revisions X-Git-Tag: Release_2_10_0~47^2~5^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ef9b1b04ed341a52cebdba245eb234c878c7d8d8;p=jalview.git JAL-1563 UniProt FTS doc revisions --- diff --git a/help/html/features/uniprotsequencefetcher.html b/help/html/features/uniprotsequencefetcher.html index 9b2e3fa..77f7b60 100644 --- a/help/html/features/uniprotsequencefetcher.html +++ b/help/html/features/uniprotsequencefetcher.html @@ -20,142 +20,150 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -The Uniprot Free Text Search Interface +The UniProt Free Text Search Interface - The Uniprot Free Text Search Interface + The UniProt Free Text Search Interface +
Since version 2.10 (September 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.

- 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").

- 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) + UniProt sequence fetcher (introduced in Jalview 2.10)

- Searching the Uniprot Database + 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. + To search UniProt, simply begin typing in the text box. After a + short delay (uabout 1.5 seconds), results will be shown in the table + below. 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.

+
  • 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 query fields for + UniProtKB): + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    human antigenAll entries containing both terms.
    human AND antigen
    human && antigen
    "human antigen"All entries containing both terms in the exact order.
    human -antigenAll entries containing the term human + but not antigen. +
    human NOT antigen
    human ! antigen
    human OR mouseAll entries containing either term.
    human || mouse
    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 -

    + 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. + +

    - 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. + 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 + The UniProt Free Test Search Interface was introduced in + Jalview 2.10.0

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