Peter & Tim,
>> what I use for current script using dna for the blast is:
>> seqret -auto -filter -osf fasta $sequence_1 > Seq1_fasta
>> seqret -auto -filter -osf fasta $sequence_2 > Seq2_fasta
>> formatdb -i Seq1_fasta -p f
> blastall -d Seq1_fasta -i Seq2_fasta -p tblastx -m 8 -o $outputfile
Instead of using 'formatdb' and 'blastall' just to BLAST one sequence
against another, I recommend using 'bl2seq' instead - it's a lesser
known command which is part of the standard BLAST suite. This removes
the need for writing (temporary) database files:
seqret -auto -filter -osf fasta $sequence_1 > Seq1_fasta
seqret -auto -filter -osf fasta $sequence_2 > Seq2_fasta
bl2seq -i Seq1_fasta -j Seq2_fasta -p tblastx -D 1
The only confusing part is that 'bl2seq' uses the "-m" parameter for
something else, so you need to use "-D 1" to do what "-m 8" usually
does. Most of the other parameters (eg. "-e") are the same.
--
Dr Torsten Seemann http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia
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