BLASTing short sequences: try Blitz

Arnoud van Vliet avvliet at knoware.nl
Wed May 26 18:45:54 EST 1999

Yep Francois,

but sometimes you just gotta try it out. Sometimes I just don't care why it
works, as long as it works. Reading the manuals of search programs like
Blitz/Blast/Fasta is not my favourite pastime, although I feel sorry for the
writers :)

I guess it's up to the person asking the question to read the manuals!


Francois Jeanmougin wrote in message <7ie81r$7r0$1 at news.u-strasbg.fr>...
>In article <927550788.415521 at news2.knoware.nl>,
> "Arnoud van Vliet" <avvliet at knoware.nl> writes:
>> Dear Mathieu
>> you could try Blitz, at the EBI site (www.ebi.ac.uk). I don't know why,
>> it has worked better for me than Fasta or Blast with a 10 AA sequence.
>> Blitz gave me a decent homology, with what later turned out to be the
>> homologue of our protein.
>> I'll leave it to the specialists to explain why.
> Please read the documentations on the softwares you use!
> It is exactly the same problem as a filtration, you chose the
>column regarding what you want to filter.
> François.

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