Sequence Fetcher

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=3eb8178713f13587151cdf9e380abec68d78e3a8;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 3eb8178..44aa1c2 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -1,72 +1,107 @@ + --> Sequence Fetcher -

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.

Database selection dialog for fetching sequences (introduced in Jalview 2.8)

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 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.

+ Every time a new fetcher is opened, you will need to select + the database you want to retrieve sequences from the database + chooser. +

+ The databases are shown as a tree, and ordered alphabetically; + tooltips are shown if you mouse over some sources, explaining what + the database will retrieve. You can select one by using the up/down + arrow keys and hitting return, or by double clicking with the mouse. +
+ If you have DAS sources enabled, then you may have several + sources for the same type of sequence identifier, and these will + be grouped together in a sub-branch branch labeled with the + identifier. +

Once you have selected a sequence database, its fetcher dialog + will open. Jalview provides two types of dialog:

The Free-text Search Interface
Free-text + search clients are provided for PDB (Since 2.9), and UniProt + (Since 2.10). They provide access to each database's own query + system, enabling you to retrieve data by accession, free text + description, or any other type of supported field. For full + details, see each client's help page: +
- PDB Sequence + Fetcher
- UniProt + Sequence Fetcher
Accession based sequence retrieval
+ +
To + retrieve sequences, simply 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.

+ Only retrieving part of a sequence +

+ When using DAS sources (indicated by a "(DAS)"), + you can append a range in addition to a sequence ID. For example, 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)