X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=4aa72344b9981ffde1892f522dc7eafd6f868c74;hb=1f46c912a14d05f673e19b272fec4e6094874fa5;hp=89b3d3bb65c1be2d052ac55675ae2c5e115f66be;hpb=11d7be472ca5ea89d69e5bb7882c0058b2c3c4b9;p=jalview.git diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 89b3d3b..4aa7234 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -23,32 +23,48 @@
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 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.
- -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.
++ 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 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. +
+ +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. +
Fetching from The PDB with the EMBL-EBI PDBe Search Interface @@ -70,13 +86,14 @@ DBFetch service provided by the EMBL European Bioinformatics Institute, or, sinc 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)
-
+
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)