[Bioperl-l] New modules

[Brian Osborne]

Rob,

Can the repeats overlap? There was a recent feature request for something
like this...

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Rob Edwards
Sent: Saturday, October 18, 2003 10:53 PM
To: Bioperl
Subject: [Bioperl-l] New modules

I have written a couple of modules that are bioperl-ish. They are by no
means finished, polished objects, and there is not t/ scripts at the
moment. (But there are some docs!).

Bio::Tools::RepeatFinder for finding direct and indirect, perfect, and
imperfect repeats in DNA sequences.

It is not necessarily speed-optimized, but it works well for sequences
upto several hundred kb. The imperfect repeats part of it (a) just
joins other repeats that it finds, so there is a limitation on the
minimum length of imperfect repeats (2n+1 where n is the user-defined
length of one half of a repeat); (b) in the current implementation
requires Tie::RefHash; (c) the distance between repeats can be
specified; and (d) this really slows things down because all the
repeats are compared to all other repeats. You don't have to calculate
these though, if you are only looking for perfect repeats.

Bio::SearchIO::Blink is a parser for BLINK from NCBI

Blink is NCBI's Blast Link - precalculated BLAST searches for every
protein in the NR database (I believe). Unfortunately these reports
don't contain useful things like starts and stops of matches so at the
moment this doesn't return a very bioperl-ish result, but I am hoping
that as NCBI develop BLINK this module can evolve into something. Its
useful as is, though, depending on what you need.

The modules are available from http://www.salmonella.org/bioperl/

Take a look and let me know what you think or if you find bugs.

Rob

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