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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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- * Jalview is free software: you can redistribute it and/or
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-<head>
-<title>Sequence Fetcher</title>
-</head>
-<body>
- <p>
- <strong>Sequence Fetcher</strong>
- </p>
- <p>Jalview can retrieve sequences from a range of sequence, 3D
- structure, genomic and domain family databases provided by EMBL-EBI.</p>
- <p>The Sequence Fetcher can be opened via the "File"
- menu on the main desktop in order to retrieve sequences as a new
- alignment, or opened via the "File" menu of an existing
- alignment to import additional sequences. There may be a short delay
- when the sequence fetcher is first opened, whilst Jalview contacts each database's web API.</p>
- <p>
- Every time a new fetcher is opened, you will need to <strong>select
- the database you want to retrieve sequences</strong> from the database
- chooser.
- </p>
- <img src="selectfetchdb.gif" align="left" width="480" height="204"
- alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
- <p>
- The databases are shown as a tree, and ordered alphabetically;
- tooltips are shown if you mouse over some sources, explaining what
- the database will retrieve. You can select one by using the up/down
- arrow keys and hitting return, or by double clicking with the mouse.
- </p>
- <p>Once you have selected a sequence database, its fetcher dialog
- will open. Jalview provides two types of dialog:</p>
- <ol>
- <li><strong>The Free-text Search Interface</strong> <br />Free-text
- search clients are provided for PDB (Since 2.9), and UniProt
- (Since 2.10). They provide access to each database's own query
- system, enabling you to retrieve data by accession, free text
- description, or any other type of supported field. For full
- details, see each client's help page:
- <ul>
- <li><a href="pdbsequencefetcher.html">PDB Sequence
- Fetcher</a></li>
- <li><a href="uniprotsequencefetcher.html">UniProt
- Sequence Fetcher</a></li>
- </ul></li>
- <li><strong>Accession based sequence retrieval</strong> <br />
-
- <img src="seqfetcher.gif" align="center"
- alt="The Jalview Sequence Fetcher Dialog Box"><br /> To
- retrieve sequences, simply <strong>enter one or more
- accession ids</strong> (as a semi-colon separated list), or press the
- "Example" button to paste the example accession for the
- currently selected database into the retrieval box. Finally, press
- "OK" to initiate the retrieval.</li>
- </ol>
-
- <p>If you use the WSDBFetch sequence fetcher services (EMBL,
- UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
- <p>
- Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
- J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
- R. <br> SOAP-based services provided by the European
- Bioinformatics Institute.<br> Nucleic Acids Res. 33(1):W25-W28
- (2005) <br> <br>
- </p>
-</body>
-</html>
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