[Bioperl-l] (no subject)

[Sendu Bala]

Luba Pardo wrote:
> Hello, I am new bioperl and I have been trying to run the examples
> available in bptutorial.pl and other basic literature. I have
> installed the latest release of bioperl 1.5.2 in a usr/local/src
> directory. Any time I try to retrieve the SwissProt and EMBL
> databases it gives me an error.

What exactly are you trying? Paste some relevant code along with the
exact error message you get when running that code.


> I wonder if the installation was not successful, as  I would expect
> that these databases accesses were included in the modules of BioPerl
> Core.

They should work with just core installed.


  In addition, I would like to ask whether to run Clustaw within
> the setting of BioPerl I need to download and install it in the same 
> directory in which I have installed bioperl, or is it included in the
> module of Bio::Align.

The ClustalW module is in the bioperl-run package, so install that in
the same way you installed bioperl (core). The actual ClustalW program 
you need to download and install according to its own instructions. You 
let Bioperl know about where you installed ClustalW by eg. setting an 
environment variable.

See 
http://doc.bioperl.org/bioperl-run/Bio/Tools/Run/Alignment/Clustalw.html#DESCRIPTION
for details.


> I am not sure whether this is the best place to ask these very basic 
> questions. If not, could anyone please refer me to the proper e mail 
> account?

Its certainly the correct place, I hope we can resolve your problems.