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
-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
+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 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
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)
+
+