The Uniprot Free Text Search Interface

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Funiprotsequencefetcher.html;fp=help%2Fhtml%2Ffeatures%2Funiprotsequencefetcher.html;h=55b4d71c31ad66b542677b8dd98ed564e1247634;hb=99ab1f82f65f725e02cf9c8ad1cbe3e16f62ad80;hp=0000000000000000000000000000000000000000;hpb=479c44e27a46c7cbee33e293dbc38cbca4fd2e0b;p=jalview.git diff --git a/help/html/features/uniprotsequencefetcher.html b/help/html/features/uniprotsequencefetcher.html new file mode 100644 index 0000000..55b4d71 --- /dev/null +++ b/help/html/features/uniprotsequencefetcher.html @@ -0,0 +1,161 @@ + + + +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 +

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