Hi, I suspect this is related to the default view used in SRS. It is returning the first page of results that contains 30 sequences (the default). To overcome this problem, the call need to have the following parameters:
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[uniprot-des:kinase]+-vn+1+-lv+100 -vn <int> is the view to use (1=names, 2=complete entries) -lv <int> is the number of entries to be used in one go It is important to realize that downloading a lot of entries, although possible, take a while and results in high loads for the servers. The way in which I use to download a large set of entries is by generating a list (using -vn 1) and then using the list with seqret in the following way: % seqret @listname -out mykinases and making sure this time that -vn 2 is used to retrieve complete entries. This requires the addition of other EMBOSS database definitions (one for lists and another for complete entry retrieval). Hope this helps, R:) Marlena Roszczyk wrote: > Does anybody know how to solve this problem: > > I use Emboss via srswww method and everything seems to work fine until I > ask seqret or infoseq (or any other application that searches the > database) for many sequences (for example typing: "seqret > database-des:kinase"). The output consists only of 30 entries even > though the same query on srs.ebi.ac.uk results in a 6-digit number of > entries. What shall I do to get all the entries I want? Is it a problem > with Emboss or rather srs policy of sending data? > > > Just in case you would like to see my emboss.default: > > DB zuniprot [ > methodquery: srswww > format: swiss > type: P > fields: "id acc sv des key org" > dbalias: uniprot > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"; > comment: "uniprot/swiss via srswww" > ] > > DB zswiss [ > methodquery: srswww > format: swiss > type: P > fields: "id acc sv des key org" > dbalias: swissprot > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"; > comment: "swissprot via srswww" > ] > > DB zembl [ > type: N > methodquery: srswww > format: embl > fields: "id acc key sv des org" > dbalias: embl > url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"; > comment: "embl via srswww" > ] > > > Thanks in advance, > Marlena Roszczyk > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
