The UniProt Free Text Search Interface

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Funiprotsequencefetcher.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Funiprotsequencefetcher.html;h=72e7649a1b429f6895e2810f1d41b3c886a63f87;hb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;hp=0000000000000000000000000000000000000000;hpb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;p=jalview.git diff --git a/help/help/html/features/uniprotsequencefetcher.html b/help/help/html/features/uniprotsequencefetcher.html new file mode 100644 index 0000000..72e7649 --- /dev/null +++ b/help/help/html/features/uniprotsequencefetcher.html @@ -0,0 +1,169 @@ + + + +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. +

+ 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 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 be displayed or removed.

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

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