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This is the README file for the Bioperl central distribution. # $Id$ o Version This is Bioperl version 1.2.3., a stable bug fix release. o Getting Started Thanks for downloading this distribution! For tutorials see Bioperl's bptutorial.pl (in this directory) or howto documents in docs/howto or from our website at http://bioperl.org/Docs and http://bioperl.org/HOWTOs. An online Bioperl tutorial at http://www.pasteur.fr/recherche/unites/sis/formation/bioperl is also available. For information on databases and Bioperl see biodatabases.pod. To look at example code browse the scripts/ directories, and look at bioscripts.pod for a descriptions of all these scripts. The bioperl.pod file also gives a overview of the history and purpose of Bioperl. The FAQ may also be useful if you have a particular question. For people starting out with Perl and Bioperl, look at the Bio::Perl module (go perldoc Bio::Perl from the directory you are reading this file in). This module is designed to flatten the learning curve for newcomers. For a discussion of issues in design and development please see biodesign.pod, recommended for those who want to contribute code. And for a list of OS's and versions that are known to support Bioperl see the PLATFORMS file. For info on Bioperl read on! o About Bioperl Bioperl is an association of developers of public domain Perl tools for computational molecular biology. Our website http://bioperl.org provides an online resource for modules, scripts, and web links for developers of Perl-based software for life science research. o Contact info Bioperl developers: firstname.lastname@example.org There's quite a variety of tools available in Bioperl, and more are added all the time. If the tool you're looking for isn't described in the documentation please write us, it could be undocumented or in process. Project website : http://bioperl.org Project FTP server: bioperl.org (anonymous FTP ok) Bug reports : http://bugzilla.bioperl.org/ email@example.com Please send us bugs, in particular about documentation which you think is unclear or problems in installation. We are also very interested in functions which don't work the way you think they do! Please see the AUTHORS file for the complete list of bioperl developers and contributors. Please see the INSTALL document for installation instructions. o About the directory structure The bioperl directory structure is organised as follows: Bio/ - Bioperl modules models/ - DIA drawing program generated OO UML for bioperl classes t/ - Perl built-in tests t/data/ - Data files used for the tests - provides good data examples for those new to bioinformatics data. scripts/ - Resuable scripts that use bioperl, some organisation in attempted here (i.e. das contains das related scripts) scripts/contributed - User submissions of useful scripts not necessarily integrated into bioperl. Please see the README in this directory. doc/ - "How To" files and the FAQ as XML o Documentation The "meta" documentation can be found in the bioperl.pod file. This should be the starting point for you to read about what bioperl is, how to use it and who wrote it. The bptutorial.pl file is a POD formatted tutorial document that contains useful information for new and existing Bioperl users. This file also contains a number of useful scripts that the student of Bioperl may want to examine. Use your favorite pod2* translator turn it into the format of choice or view it directly via perldoc. For example, go perldoc bioperl or in this directory go pod2text bioperl.pod | more pod2text bptutorial.pl | more pod2html, which comes with Perl, can be used to create web-browser navigable documentation files. Individual *.pm modules have their own embedded POD documentation as well. A complete set of hyperlinked POD, or module, documentation is available at http://www.bioperl.org. The most up-to-date Remember 'perldoc' is your friend. You can use this to read any file containing POD formatted documentation without needing any type of translator. There is also an online course written at the Pasteur Institute. See: http://www.pasteur.fr/recherche/unites/sis/formation/bioperl. Useful documentation in the form of example code can also be found in the scripts/ directory. The current collection includes scripts that run BLAST, index flat files, parse PDB structure files, make primers, retrieve ESTs based on tissue, align protein to nucleotide sequence, run GENSCAN on multiple sequences, and much more! See bioscripts.pod for a complete listing. o Releases Bioperl releases are always available from the website http://www.bioperl.org or by FTP from ftp://bioperl.org. (Note that we've had trouble with our new network setup which is not allowing FTP to support passive mode properly: use http://www.bioperl.org/DIST to get a listing of the distribution directory). Each release is tested with the test suite and cross-tested on a number of different platforms. See the PLATFORMS file for more information on a specific platform. All efforts are made to release a bug-free package, however any known bugs in a release will be documented in the BUGS file. See the Changes file for a listing of what features have been added or what APIs have changed between releases. Like many internet projects, Bioperl now has a consistent numbering scheme to indicate stable release series vs development release series. A release number is a three digit number like 1.2.0 - the first digit indicates the major release - the idea being that all the API calls in a major release are reasonably consistent. The second number is the release series. This is probably the most important number. Even numbers here (1.0, 1.2 etc) indicate stable releases. Stable releases are well tested and recommended for most uses. Odd numbers (1.1, 1.3 etc) are development releases which one should only use if you are interested in the latest and greatest features. The final number (eg, 1.2.0, 1.2.1 etc) is the bug fix release. The higher the number the more bug fixes has been incorportated. In theory you can upgrade from one bug fix release to the next with no changes to your own code (for production cases, obviously check things out carefully before you switch over). o Caveats, warnings, etc When you run the tests (make test) often some tests will issue warnings messages or even fail. Sometimes this is because we didn't have anyone test the test system on the combintaion or your operating system, version of perl, and associated libraries and other modules. Because Bioperl depends on several outside libraries we may not be able to test every single combination (mind you, now you've tested another possible situation and we encourage you to contribute back to the development process by emailing the list or submitted a bug), so if there are warnings you will find that in fact many things are not a big deal. See the PLATFORMS file for reports of specific issues. If you install the bioperl-run system and run tests when you don't have the program installed you'll get messages like 'program XXX not found, skipping tests'. That's okay, Bioperl is doing what it is supposed to do. If you wanted to run this program you'd need to install it first. Not all scripts in the scripts directory are correct and up-to-date. We need volunteers to help maintain these so if you find they do not work, submit a bug report http://bugzilla.bioperl.org and/or consider helping out in their maintence. Don't be disuaded by a script not working, often the SYNOPSIS of the module is the best place to start when trying to learn how to use them. If you are confused about what modules are appropriate when you try and solve a particular issue in bioinformatics we urge you to look at the bptutorial first. o A simple module summary Here is a quick summary of many of the useful modules and how the toolkit is laid out: All modules are in the Bio/ namespace, - Perl is for newbies and gives a functional interface to the main parts of the package - Seq is for Sequences (protein and DNA). o Bio::PrimarySeq is a plain sequence (sequence data + identifiers) o Bio::Seq is a PrimarySeq plus it has a Bio::Annotation::Collection and a Bio::SeqFeatureI objects attatched. o Bio::Seq::RichSeq is all of the above plus it has slots for extra information specific to GenBank/EMBL/SwissProt files. o Bio::Seq::LargeSeq is for sequences which are too big for fitting into memory. - SeqIO is for reading and writing Sequences, it is a front end module for separate driver modules supporting the different sequence formats - SeqFeature - start/stop/strand annotations of sequences o Bio::SeqFeature::Generic is basic catchall o Bio::SeqFeature::Similarity a similarity sequence feature o Bio::SeqFeature::FeaturePair a sequence feature which is pairwise such as query/hit pairs - SearchIO is for reading and writing pairwise alignment reports like BLAST or FASTA - Search is where the alignment objects are defined o Bio::Search::Result::GenericResult is the result object (a blast query is a Result object) o Bio::Search::Hit::GenericHit is the Hit object (a query will have 0-> many hits in a database) o Bio::Search::HSP::GenericHSP is the High-scoring Segment Pair object defining the alignment(s) of the query and hit. - SimpleAlign is for multiple sequence alignments - AlignIO is for reading and writing multiple sequence alignment formats - Assembly provides the start of an infrastructure for assemblies and Assembly::IO IO converters for them - DB is the namespace for all the database query objects o Bio::DB::GenBank/GenPept are two modules which query NCBI entrez for sequences o Bio::DB::SwissProt/EMBL query various EMBL and SwissProt repositories for a sequences o Bio::DB::GFF is Lincoln Stein's fast, lightweight feature and sequence database which is the backend to his GBrowse system (see www.gmod.org) o Bio::DB::Flat is a fast implementation of the OBDA flat-file indexing system (cross-language and cross-platform supported by O|B|F projects see http://obda.open-bio.org). o Bio::DB::BioFetch/DBFetch for OBDA, Web (HTTP) access to remote databases. o Bio::DB::InMemoryCache/FileCache (fast local caching of sequences from remote dbs to speed up your access). o Bio::DB::Registry interface to the OBDA specification for remote data sources o Bio::DB::XEMBL SOAP access to sequence databases o Bio::DB::Biblio for access to remote bibliographic databases. - Annotation collection of annotation objects (comments, DBlinks, References, and misc key/value pairs) - Coordinate is a system for mapping between different coordinate systems such as DNA to protein or between assemblies. - Index is for locally indexed flatfiles with BerkeleyDB - Tools contains many misc parsers and function for different bioinformatics needs o Gene prediction parser (Genscan, MZEF, Grail, Genemark) o Annotation format (GFF) o simulate RE cutting with RestrictionEnzyme o Enumerate codon tables and valid sequences symbols (CodonTable, IUPAC) o Phylogenetic program parsing (PAML, Molphy, Phylip) - Map genetic and physical map representations - Graphics render a sequence with its features in the standard 'tracks'gram. - Structure - parse and represent protein structure data - TreeIO is for reading and writing Tree formats - Tree is the namespace for all the associated Tree objects o Bio::Tree::Tree is the basic tree object o Bio::Tree::Node are the nodes which make up the tree o Bio::Tree::Statistics is for computing statistics for a tree o Bio::Tree::TreeFunctionsI is where specific tree functions are implemented (like is_monophyletic and lca) - Bio::Biblio is where bibliographic data and database access objects are kept - Variation represent sequences with mutations and variations applied so one can compare and represent wild-type and mutation versions of a sequence. - Root, basic objects for the internals of Bioperl o Upgrading from an older version If you have a previously installed version of bioperl on your system some of these notes may help you. Some modules have been removed because they have been superceeded by new developement efforts. They are documented in the DEPRECATED file that is included in the release. In addition some methods, or the Application Programming Interface (API), have changed or been removed. You may find that scripts which worked with bioperl 1.0.2 may give you warnings or may not work at all (although we have tried very hard to minimize this!). Send an email to the list and we'll be happy to give you pointers.