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. 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+
+ Sequence Fetcher
-
- 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)
-
+
+ Jalview can retrieve sequences from certain databases using either + the DBFetch service provided by the EMBL 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. +
++ Fetching from The PDB with the EMBL-EBI PDBe Search + Interface +
++ Since Jalview 2.9, selecting PDB as the sequence database will open + the PDB Sequence Fetcher for + discovering and retrieving structures. +
++ 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, 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)