[Bioperl-l] All-vs-all BLAST

[James Wasmuth]

Although I am going to support Aaron's call earlier today about using 
Ssearch for pairwise comparison, the increase in accuracy is worth the 
slight increase in time...

Tony Andreeva wrote:

> To be more precise:
>
> Use bl2seq if you want to compare each two pairs. using bl2seq you 
> will avoid formatting
>
> % bl2seq -p blastp -i sequence1 -j sequence2 -o seq1-vs-seq2.out ( and 
> suitable parameters )
>
>
> Use blastall if you want to search with each sequence against the others
>
> % formatdb -i seq.db -o T
> % blastall -p blastp -i seq.db -d seq.db -o seq.out ( and suitable 
> parameters )
>
> By simply typing:
>
> %blastall --help
> or
> %bl2seq --help
>
> you can obtain quite detailed help for the program settings.
>
> Hope that helps
> Tony
>

-- 
I like nonsense, it wakes up the brain cells.
		-- Dr. Seuss

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