[Biopython-dev] PolyA Sequence fails to BLAST?

[João Rodrigues]

Hello all, this is quite a general curiosity.

I was trying my application and I was testing the case of a sequence not
having matches in BLAST. I chose a long stretch of Alanines, randomly:
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

This is the URL that Biopython generated (printed from NCBIWWW.py):

http://blast.ncbi.nlm.nih.gov/Blast.cgi?COMPOSITION_BASED_STATISTICS=True&DATABASE=pdb&ENTREZ_QUERY=%28none%29&EXPECT=10&GAPCOSTS=10+1&HITLIST_SIZE=50&MATRIX_NAME=PAM70&PROGRAM=blastp&QUERY=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA&WORD_SIZE=3&CMD=Put

Not finding this odd enough, because it says "Sequence not in FASTA format",
I went to the BLAST server page and manually tried to run it. Same error.

My question is not related to BioPython, but since I found it with it, I
guess I might as well ask:

Why does a poly A sequence crashes BLAST? :x

Regards!

João [ .. ] Rodrigues

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