[Bioperl-l] Newbie Q's

[Jason Stajich]

On 5 Sep 2002, Pat Schloss wrote:

> Hi,
>
> I'm having a bit of trouble installing everything that's necessary for
> running bioperl.  What I'd like to do is submit sequences for BLASTing
> and then manipulate the output.  I downloaded and un-tar-ed the main
> file from bioperl.org and it is currently residing in
> /usr/local/src/bioperl-1.0.2.  I also installed the bundle from CPAN.

You mean the BioPerl::Bundle?  you can also install bioperl from cpan if
you like - otherwise make sure you have set the env variable
PERL5LIB=/usr/local/src/bioperl-1.0.2
(this is actually the best way so that upgrading bioperl is as simple as
updating the env variable -- but harder when you setup a system for many
users)

To check that your bioperl is installed and your perl knows where it is do
% perldoc Bio::Seq


> Finally, I also downloaded blast.linux.tar.Z and un-tar-ed it in

> /usr/local/src.  So I'm not sure if what I've done is correct.  Any
> suggestions on how to check?
>

You don't actually need bioperl necessarily to run blast, in fact, if
you've never run it locally you should probably do it on the cmd line
before doing it within bioperl.   This is a good skill to have and will
let you check that everything is working.

See the README.bls in the blast dir on how you need you setup you
~/.ncbirc and your blastable dbs.  Download a database from NCBI -
/blast/db/ecoli.aa.Z is a good starting one.  Put it in
/usr/local/src/blast/data (unless you're getting fancier with how you are
setting up your blast exe and defining env variables like BLASTDB).

Examples of how to use bioperl to parse your blast report see the
bptutorial and Bio::SearchIO documentation.  My simple HowTO on SearchIO
http://www.bioperl.org/HOWTOs/SearchIO/use.html (which will get fleshed
out a bit more one day) has simple cut-and-paste block of code that gets
you started.

Later when you are comfortable with this you can see the
Bio::Tools::Run::StandAloneBlast but I wouldn't start with this.

> Also, is there a somewhat clearcut explanation somewhere of how to BLAST
> a couple sample sequences and retrieve the information?  I've read
> through Tisdall's _Beginning Perl..._ book and O'Reilly's other book
> _Learning Perl_.  So that's my level of expertise and am still unsure
> how modules and remote access of databases works.  Any thoughts on how
> to other sources of information?

bptutorial which is included in the distribution
% perldoc /usr/local/src/bioperl-1.0.2/bptutorial.pl

>
> Thanks,
> Pat
>
>
>
>
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>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu