From: jprocter Date: Tue, 5 Aug 2008 15:32:09 +0000 (+0000) Subject: new sequence fetcher documentation X-Git-Tag: Release_2_4~62 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=169747b5aac00cb86214916fdfc653a2be26ed92;p=jalview.git new sequence fetcher documentation --- diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index fe1cfb8..135e4d5 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -1,27 +1,34 @@ - -Sequence Fetcher - -

Sequence Fetcher

-

Jalview can retrieve sequences from certain databases via the -WSDBFetch service provided by the European Bioinformatics Institute.

-

A 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. -

-

Select the database you want to retrieve sequences from, and enter - the database id (or a semi-colon separated list of several ids) in - the text 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 sequence fetcher 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 + +

Sequence Fetcher

+

Jalview can retrieve sequences from certain databases using either the +WSDBFetch service provided by the European Bioinformatics Institute, and DAS servers capable of the sequence command (since version 2.4).

+The Jalview Sequence Fetcher Dialog Box +

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.

+

+ 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

When retrieving from DAS sequence sources, + coordinate range arguments can be passed to the server using the standard DAS + sequence command format (:<start>,<end>)

+

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)
+
+

+ + diff --git a/help/html/features/seqfetcher.gif b/help/html/features/seqfetcher.gif new file mode 100644 index 0000000..809d719 Binary files /dev/null and b/help/html/features/seqfetcher.gif differ