[BioC] Automated blasting of short nucleotide sequences against each other

[Ken Termiso]

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