Hi All,
I know this should be simple, but I just can't find an example of how to do this.. I'll keep looking, but hoped it might save time if someone already knew..
I was to run blastx on about 1.3M reads, so thought I might speed it up by using a smaller database or masking 'nr'. The BLAST manual shows ways to mask low complexity, but is there a way to only look for a certain taxon hit?
I have tried to D/L by entrez all the seqs for the taxon (familly level) that I am interested in, but the D/L goes very slow from NCBI until it gets to about 4k/s ! I have always had that problem when trying to D/L a lot from Entrez searches, I guess it must be some kind of restriction..
Thanks for any help!
S.
I know this should be simple, but I just can't find an example of how to do this.. I'll keep looking, but hoped it might save time if someone already knew..
I was to run blastx on about 1.3M reads, so thought I might speed it up by using a smaller database or masking 'nr'. The BLAST manual shows ways to mask low complexity, but is there a way to only look for a certain taxon hit?
I have tried to D/L by entrez all the seqs for the taxon (familly level) that I am interested in, but the D/L goes very slow from NCBI until it gets to about 4k/s ! I have always had that problem when trying to D/L a lot from Entrez searches, I guess it must be some kind of restriction..
Thanks for any help!
S.
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