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. +
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)
+
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)
-
-