[BioC] Automated blasting of short nucleotide sequences againsteach other

[David Lapointe]

Well, you only need one run. A query of 500 short seqs against a database of 
the 500 short seqs.   See 
http://www.oreillynet.com/pub/a/oreilly/bio/news/BLAST.html

for a great example. ( Blasting Y.Pestis Proteome vs E.Coli proteome ~ 4000 
seqs each, takes about 3-4 min on  my laptop).  BLASTCLUST might also do what 
you need.

David
On Friday 18 February 2005 02:41 pm, Ken Termiso wrote:
> Hi all,
>
>  This may be slightly off-topic, but I'd like to be able to BLAST a large
> set of about 500 nucleotide sequences against itself (i.e. sequence #1 gets
> blasted against the other 499 sequences and so on, for a total of 500x500
> or 250,000 blasts), and one thing I unbelievably cannot google on the net
> is a script to do it...rather than writing one I was hoping that someone
> could point me to a link for this...I found tons of scripts for doing it
> against a database, but nothing with a matrix like I need to BLAST...
>
>  My sequences are in plain text. I've got the standalone blast, but just
> need a script...
>
>  Presumably this would be very useful for analyzing pseudo-homologous probe
>  sequences..?..so maybe it isn't completely off-topic...
>
>  Thanks in advance,
>  Ken
>
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