X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=44aa1c213a8f4f8c42c273b1c18d85855a74b4e8;hb=e0fd9965a1ffacf4ac034a79e7cb5f7e898ff69f;hp=b14f0dc611861c86b4932f420cdff31a78cf43b3;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index b14f0dc..44aa1c2 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -1,51 +1,107 @@ -Sequence Fetcher + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +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 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)
-
+

+ 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 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. +

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

+ 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:

+
    +
  1. 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: +
    2. +
  2. Accession based sequence retrieval
    + + The Jalview Sequence Fetcher Dialog Box
    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.
    3. +
+

+ 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)