Bio-Grep version 0.8.4 ====================== Bio-Grep is a collection of Perl modules for searching in Fasta files. 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 but requires no additional software. 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. 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. Hypa (http://bibiserv.techfak.uni-bielefeld.de/HyPa/) Another powerful enhanced suffix array tool. We use only a small set of features. Hypa is not yet offically released. It supports wobble pairs, meaning that GU mismatches can count only 0 or 0.5 mismatches. Another difference is that you can define how many insertions and deletions should be allowed. The other back-ends only allow edit or hamming distances. The tests require that hypa is in your path. ...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, or through the web interface at L. COPYRIGHT AND LICENCE 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.