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)
-
-
+ Sequence Fetcher +
++ 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)
+