X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=135e4d57d49bb877c74c3895c9eecd41321bfab6;hb=0942955908d861c8f85b3c6f9825fbcc49eac371;hp=02ff94ed7cdf32d44b3444dd073f613fd9ce4042;hpb=f7fd2fcf425c4a599dbb1440678672eb31cd865a;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 02ff94e..135e4d5 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -1,19 +1,34 @@ - -Sequence Fetcher - -

Sequence Fetcher

-

The Sequence Fetcher can be started from the main desktop "File" - menu or from a particular alignment window.

-

Select which database to fetch your sequence from and enter the sequence id. - If you are retrieving sequences from PDB database and you know which chain you - would like to retrieve, append the chain id after colon to the PDB id. eg 1GAQ:A

-

The Sequence Fetcher uses WSDBFetch provided by the European Bioinformatics - Institute. If you use this service please quote:

-

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)
+
+

+ +