Bio-Grep version 0.10.1
=======================

Bio-Grep is a collection of Perl modules for searching in DNA and protein
sequences. It supports different back-ends, most importantly some (enhanced) 
suffix array implementations. Currently, there is no suffix array tool that
works in all scenarios (for example whole genome, protein and RNA data). 
Bio::Grep provides a common API to the most popular tools. This way, you 
can easily switch or combine tools.


DEPENDENCIES

This module requires these other modules, libraries and programs:


  Bioperl 1.4 http://bioperl.org/Core/Latest/index.shtml
    (You will need "Core" and "Run") Be sure that you have all
    required modules installed. You don't need to worry about this if 
    you follow all installation steps in the Bioperl Documentation 
    (for example you will need some XML modules. Bundle::BioPerl 
    will install them).
    Works with Bioperl 1.5.2.
    
  EMBOSS (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-latest.tar.gz)


  The back-ends:
  
  You need at least one of them. Vmatch is always a good choice. Agrep is
  the best choice if you allow many mismatches in short sequences, if you
  want to search in Fasta files with relatively short sequences (e.g
  transcript databases) and if you are only interested in which sequences
  the approximate match was found. Its performance is in this case 
  amazing. If you want the exact positions, choose vmatch. If you want 
  nice alignments, choose vmatch too (EMBOSS can automatically align the 
  sequence and the query in the agrep back-end, but then vmatch is faster). 
  Filters require exact positions, so you can't use them with agrep. 
  This may change in future version or not.
  GUUGle is the best choice if you have RNA queries (counts GU as no mismatch)
  and if you are interested in only exact matches.

  RE (perldoc perlre) for Perl regular expressions. A slow sliding window
      algorithm that searches all sequences for the specified regular
      expression. Compared to suffix arrays this is really slow for (nearly)
      perfect matches and large databases but requires no additional software.
      Currently it stores all hits of one sequence in memory. So this could be
      a problem for Fasta files with huge sequences (For example whole
      chromosomes as one sequence).

  Vmatch (http://vmatch.de/) for the Vmatch back-end. Commercial software.
    The Vmatch tests assume that vmatch is in your path (You
    can later specify a path to vmatch that is not in your path. 
    The tests will fail but the module should work if the 
    specified path to vmatch is correct.). 
 
  Agrep (http://www.tgries.de/agrep/) for the Agrep back-end. There
    are packages for some Linux distributions available (Debian:
    apt-get install agrep). Fink has some packages for Mac OS X.
    Ebuilds for Gentoo are available, too. As for Vmatch, Agrep 
    tests assume that agrep is in your path. 
    The TRE-agrep (http://laurikari.net/tre/) is much slower but has
    more features and less limitations. 

  GUUGle (http://bibiserv.techfak.uni-bielefeld.de/guugle/)
    A suffix array implementation for RNA sequences. Only allows search
    for exact matches. It is very memory efficent and needs no precalculated
    suffix arrays. Open Source.

  ...and other Perl modules. You will get a warning about missing
  modules when you run the make command. A lot of dependencies, we know,
  but most of them are standard software in bioinformatics. So please
  check if some of them are already installed on your workstation.


INSTALLATION

To install this module type the following (AFTER the installation of
the software in the "Dependecies"-section):

   perl Makefile.PL
   make
   make test  (optional, but highly recommended*)
   make install

Alternatively, to install with Module::Build, you can use the following
commands:

    perl Build.PL
    ./Build
    ./Build test
    ./Build install


* Bio::Grep needs a lot of other software. It is very likely that 
some problems with the installation of the dependecies show up!


DOCUMENTATION


1. Tutorials
------------

bgrep is an example implementation. The source code is well documented, so
maybe it is a good starting point.

A not yet comprehensive coobook is available in perldoc Bio::Grep::Cookbook.
Please contribute recipes if you can!


2. Performance
--------------

2.1 Vmatch


*  Try $sbe->settings->showdesc(200) if you don't need upstream or downstream
   regions. This makes the parser get all data direcly out of vmatch output.
   Otherwise the parser will call vsubseqselect for every search result.

*  Try $sbe->settings->online(1) if you allow many mismatches.


3. FAQ
------

- Is it possible to get the coordinates of the hit out of the alignment?
  Yes. $res->alignment->get_seq_by_pos(1)->...

  see perldoc Bio::SimpleAlign


BUGS

Please report any bugs, recipes for the cookbook or feature requests to
C<bug-bio-grep@rt.cpan.org>, or through the web interface at
L<http://rt.cpan.org>. 


COPYRIGHT AND LICENCE

Copyright (C) 2007 by M. Riester. All rights reserved. 

Based on Weigel::Search v0.13, Copyright (C) 2005-2006 by Max Planck 
Institute for Developmental Biology, Tuebingen.

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.4 or,
at your option, any later version of Perl 5 you may have available.

