Sequence Fetcher
-Jalview can retrieve sequences from certain databases using -either the WSDBFetch service provided by the European Bioinformatics -Institute, and, since Jalview 2.4, DAS servers capable of the sequence -command (configured in DAS settings).
-
-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.
-Fetching Individual PDB Chains
-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- -
Retrieving parts of large sequence records
-When retrieving from DAS sequence sources, coordinate range arguments
-can be passed to the server using the standard DAS sequence command
-format:
- <AccessionId>:<start>,<end>If you know a source -understands this type of query format, then you should untick the -checkbox for 'replace commas with semi-colons' so the range query can be -passed to the server; otherwise, the query will be split into two (e.g -'Mito:1' and '85779' rather than 'Mito:1,85779'). In most cases, -however, a source that supports range queries will include a range -qualification in its example query, and Jalview will then automatically -disable the 'replace commas with semi-colons' option.
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)
-
+
Jalview can retrieve sequences from certain databases using either the +WSDBFetch service provided by the European Bioinformatics Institute, or, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).
+
+ 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. There may 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 + by clicking the button labeled 'Select database retrieval source'. If + a database source is already selected, then the button's label will + change to show the currently selected database.
+
+ Since Jalview 2.8, the + available databases are shown as a tree in a popup dialog box. The + databases are ordered alphabetically, and if there are many sources + for the same type of sequence identifier, they will be grouped + together in a sub-branch branch labeled with the identifier.
+Once you have selected the sequence database using the popup dialog box, 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.
+Specifying chains for PDB IDs
+ 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+ +
+ Only retrieving part of a sequence DAS sources
+ (indicated by a "(DAS)") allow a range to be
+ specified in addition to a sequence ID. To retrieve 50 residues
+ starting at position 35 in UNIPROT sequence P73137 using the UNIPROT
+ DAS server, you would enter "'P73137:35,84'.
Full support for DAS range queries was introduced in Jalview 2.8
+
If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM) + 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)
+
+