[Bioperl-l] help with remote blast

Barry Moore barry.moore at genetics.utah.edu
Wed Sep 15 00:22:12 EDT 2004


A couple of suggestions for figuring it out yourself - both of which you 
may have already done.  First, on a module new to me I'll usually look 
at the synopsis, description and methods to try to figure out what can 
be done with this module.  For instance on your problem with reading in 
a fasta file.  You'll want to use Bio::SeqIO (found here 
http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html).  Looking at 
the doc page for that one the synopsis a description give a good idea of 
what it does, and some example script of how to do it.  But they don't 
cover all that is possible.  You had a problem with the module 
"guessing" incorrectly that your sequence was protein.  In the methods 
you see that there is an method to set the alphabet.  Accompanying that 
is usage, a one line example, returns, args, throws etc.  From that you 
can deduce that if you add a line
$seqio->alphabet('dna') to the synopsis script you will force the parser 
to interpret you seq as DNA.

The second suggestion is to check out script that are kept in the 
examples and scripts directories of the bioperl-live CVS (found here 
You can glean alot about usage from seeing how people use even seemingly 
unrelated scripts.

If you want to discuss this more, write back to the list or write me 


Michael S. Robeson II wrote:

> 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
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Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

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