[Bioperl-l] help with remote blast
Michael S. Robeson II
popgen23 at mac.com
Tue Sep 14 23:54:59 EDT 2004
I have been using perl for a while and have become somewhat comfortable
with the language, though i have much to learn. However, I have been
reading all of the bioperl documentation on remote BLAST in particular
and... all I have to say is, "for the first time I have no idea what
ya'll are talking about!" :-)
I am new to the bioperl community and I have been trying my best, but
the documentation is quit confusing to me.
All, I am trying to do is set up a way in which I can automatically
BLAST a set of sequences in a multi-sequence FASTA file. I have seen
the "Read_all_Sequences" commands but every time I use them I get an
error saying that nucleotide data is being submitted for protein data
when in fact i am sending nucleotide data and the fact that the
tutorial states that the default setting should be "nr"! I can not
find any clear documentation or examples on the bioperl web site,
tutorial, or perldocs that can even help me get started.
I have setup and run all the tutorial scripts just fine. Problem is I
have no idea how to modify the perl scripts w/o breaking them
unlearning what I have learned from them. Are there any other external
bioperl references or suggestions from the community?
I do not want the answer, I really want to figure this out on my own. I
think I just need a little nudge in the write direction to get me
started. It's just that, from my limited experience reading the bioperl
documentation, it is a world different from reading generic perl
documentation. So, any help with the "Rules of Engagement" when reading
this documentation would be a life saver!
- Thanks for any help!
- A totally lost bioperl newbie!
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