From 169747b5aac00cb86214916fdfc653a2be26ed92 Mon Sep 17 00:00:00 2001
From: jprocter Sequence Fetcher Jalview can retrieve sequences from certain databases via the
-WSDBFetch service provided by the European Bioinformatics Institute. A Sequence Fetcher dialog box 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.
- Select the database you want to retrieve sequences from, and enter
- the database id (or a semi-colon separated list of several ids) in
- the text box. Finally, press OK to initiate the retrieval.
- If you are retrieving sequences from the PDB, you can retrieve
- specific chains by appending a colon and the chain id to the PDB
- id. For example : 1GAQ:A
If you use the sequence fetcher in work for publication, please cite:
-Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
- S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.
- SOAP-based services provided by the European Bioinformatics Institute.
- Nucleic Acids Res. 33(1):W25-W28 (2005)
-
-
Sequence Fetcher
+Jalview can retrieve sequences from certain databases using either the +WSDBFetch service provided by the European Bioinformatics Institute, and DAS servers capable of the sequence command (since version 2.4).
+ +The Sequence Fetcher dialog box 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. Please note, there will be a short delay when the sequence fetcher is first opened, + whilst Jalview compiles the list of available sequence datasources from the + currently defined DAS server registry. +
+First, select the database you want to retrieve sequences from. Then, enter + one or more accession ids (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.
+
+ If you are retrieving sequences from the PDB, you can retrieve
+ specific chains by appending a colon and the chain id to the PDB
+ id. For example :
1GAQ:A
If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB and PFAM) + in work for publication, please cite:
+Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
+ S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.
+ SOAP-based services provided by the European Bioinformatics Institute.
+ Nucleic Acids Res. 33(1):W25-W28 (2005)
+
+
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