[Bioperl-l] Re remote blast

[Ewan Birney]

On Tue, 31 Dec 2002, Clement Mesdon wrote:

> Thank you for your answer
> So, first I downloaded the blast last version from NCBI, and untar it in
> /root/blast folder, no further installation seemed to be required
> Then I re installed the last version of bioperl by Perl Makefile.PL and make
> and make instaIl
> I saw that I should specify where is my blast located by doing:
> export BLASTDIR=/root/blast   that I did before installation
> but when I run the remoteblast example in bptutorial i got error message
> saying me "Can't find nextobject at line 2000 something.
>

RemoteBlast does not require you to have BLAST installed. It works via
http against the servers at NCBI. You do not have to have anything but LWP
package in Perl installed to use this.


StandAloneBlast uses local blast databases and local blast executables. If
you don't have it installed... then you are probably in one of two
situations:

  (a) You are on a machine with bioinformatics support, but you don't
know where the local blast databases are kept and the blast executable;
talk to your local bioinformatics database administrator (eg, the person
who emails the institute and says "new version of swissprot is now
available..."). Have a chat with this guy/girl about this.


  (b) You are new to bioinformatics and wanting to check everything out.
In which case, don't worry about it so much - use the RemoteBlast package
(but with care, as extensive use of it is an abuse of the service that
NCBI provides) and don't worry about setting up a local BLAST
installation until you have got a little further in.

I would also recommend buying some introduction to bioinformatics books,
of which I think the Oreilly one (Cynthia Gibas) or the one by Francis
Ouliette or Andy Baxevenis (now I am associated gently with Oreilly I get
a bit worried about recommending things - does anyone else know a good
primer for bioinformatics?)


ewan


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