[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!
- Mike

More information about the Bioperl-l mailing list