Hi,
I have been trying to update my sequence datasets using the seqret program. Step 1 is that I blast my sequence against uniprot using the EXPASY server. Unfortunately, because the recent explosion of duplicate data ("environmental samples"), it is now necessary to download 1-2K sequences and then filter out the random "environmental" sample derived fragments etc. Step 2 is assembling a list in gnumeric, exporting it as a multiline text file of format "unpirot:accession" . Step 3 is using the command "seqret @filename.txt". This is extraordinarily slow. It takes >12 hours to download a fasta file containing 3K sequences. Is there a way of speeding this up? I used to be able to download directly from EXPASY, but the site now only allows about 200-odd sequences to be selected and downloaded at a time. Note that filtering sequence sets is very fast with the program cd-hit. This takes about 10 seconds on an old P4 machine to remove sequences from the set with >90% identity to any other, for example. I do not have the resources to install and index local databases. Thanks! Richard A. Rothery, Ph.D. Research Associate ______________________________________________ Membrane Protein Research Group, Department of Biochemistry, University of Alberta, Edmonton T6G 2H7 Ph. 780-492-2229 Fax. 780-492-0886 ______________________________________________ _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss