Richard Rothery wrote:
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.
Perhaps we can download in batches ... what is your EMBOSS database definition for uniprot?
Also, how do you select the 1-2K sequences?
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.
Would this be a useful addition to EMBOSS? For example an application that reads selected entries from a database (uniprot) and filters them.
The output would be a sequence file containing the uniprot entries you need (so no need for the final seqret step retrieving sequences again).
I do not have the resources to install and index local databases.
No problem - we try to support users in exactly your situation. regards, Peter Rice _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
