BIOPERL(1)

NAME
Bioperl - Coordinated OOP-Perl Modules for Biology

SYNOPSIS
Not very appropriate to put a synopsis - many different objects to use. Read on...

DESCRIPTION
Bioperl contains a number of Perl objects which are useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are advertised to do in the documentation, but they also interact - Alignment objects are made from the Sequence objects and so on. This means that the objects provide a coordinated framework to do computational biology.

If you are new to bioperl, reading biostart.pod will get you aquainted with writing scripts and the main players for the objects.

We now also have a cookbook tutorial in bptutorial.pl which has embedded documentation. Start there if learning-by-example suites you most

Bioperl development is focused on the objects themselves, and less on the scripts (programs) that put these objects together. There are some example scripts provided in the distribution, but it is not the focus of the objects that are distributed. Of course, as the objects do most of the hardwork for you, all you have to do is combine a number of objects together sensibly.

The intent of the bioperl development effort is to make reusable tools that aid people in creating their own site or job specific applications.

The bioperl.org (http://bioperl.org) website also attempts to maintain links and archives of standalone bio-related perl tools that are not affiliated or related to the core bioperl effort. Check the site for useful code ideas and contribute your own if possible.

INSTALLATION
The Bioperl modules are distributed as a tar file that expands into a standard perl CPAN distribution. Detailed installation directions can be found in the distribution README file.

The Bioperl modules can now interact with local flat file databases. To learn how to set this up, look at the bioback.pod documentation (perldoc bioback will work once it has been installed. Alternatively go perldoc bioback.pod directly).

GETTING STARTED
The best place to start is by reading and running the cookbook script, bptutorial.pl

The directory scripts/ have fully working, industrial strength scripts for use with bioperl. These are documented ('perldoc scriptname' will work). This area only started in the 0.05 distribution, and so not that many scripts have been written (you are more than welcome to contribute!)

The example scripts in the distribution examples/ directory and sub directories therein give you an idea of how to use some of the modules and driver code.

If you have installed bioperl in the standard way, as said in the README in the distribution these examples should work by just running them. If you have a not installed it in a standard way you will have to change the 'use lib' to point to your installation.

examples/rev_and_trans.pl - examples using Bio::Seq.pm for reversing and translating sequences

examples/restriction.pl - example code for using the Bio::Tools::RestrictionEnzyme.pm module.

examples/simplealign.pl - example code for using the Bio::SimpleAlign module.

examples/psw.pl - example code for using the XS extensions for a Protein Smith-Waterman comparison.

examples/blast/ - example code for using the Bio::Tools::Blast.pm module.

examples/seq/ - example code for working with multiple sequence files.

examples/root_object/ - example code for using Bio::Root::Object.pm.

GETTING INVOLVED
Bioperl is a completely open community of developers. We are not funded and we don't have a mission statement. We encourage collaborative code, in particular in perl. You can help us in many different ways, from just a simple statement about how you have used bioperl to do something interesting to contributing a whole new object hierarchy. See http://bioperl.org for more information. Here are some ways of helping us

  Telling us you used it
We are very interested to hear how you experienced using bioperl. Did it install cleanly? Did you understand the documentation? Could you get the objects to do what you wanted it to do? If bioperl was useless we want to know why, and if it was great - that too. Post a message to bioperl-l@bioperl.org (the bioperl mailing list, where all the developers are).

Only by getting people's feedback do we know whether we are providing anything useful.

  Writing a script that uses it
By writing a good script that uses bioperl you both show that bioperl is useful and probably save someone elsewhere writing it. If you contribute it to the 'script central' at http://bioperl.org then other people can view and use it

  Find bugs!
We know that there are bugs in there. If you find something which you are pretty sure is a problem, post a note to bioperl-bugs@bioperl.org and we will get on it as soon as possible. (you can also access the bug system through the web pages).

  Suggest new functionality
You can suggest areas where the objects are not ideally written and could be done better. The best way is to find the main developer of the module (each module was written principly by one person except for Seq.pm). Talk to him or her and suggest changes.

  Make your own objects
If you can make a useful object we will happily include it into the core. Probably you will want to read alot of the documentation in the Bio::Root section and also talk to people on the bioperl mailing list bioperl-l@bioperl.org

biodesign.pod provides documentation on the conventions and ideas used in bioperl. It is definitely worth a ready if you are interested in contributing.

CONVENTIONS

  Alphabets
Bioperl modules use the standard extended single-letter genetic alphabets to represent nucleotide and amino acid sequences.

In addition to the standard alphabet, the following symbols are also acceptable in a biosequence:

 ?  (a missing nucleotide or amino acid)
 -  (gap in sequence)

  Extended Dna / Rna alphabet
 (includes symbols for nucleotide ambiguity)
 ------------------------------------------
 Symbol       Meaning      Nucleic Acid
 ------------------------------------------
  A            A           Adenine
  C            C           Cytosine
  G            G           Guanine
  T            T           Thymine
  U            U           Uracil
  M          A or C
  R          A or G
  W          A or T
  S          C or G
  Y          C or T
  K          G or T
  V        A or C or G
  H        A or C or T
  D        A or G or T
  B        C or G or T
  X      G or A or T or C
  N      G or A or T or C
 IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE:
   Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030.

  Amino Acid alphabet
 ------------------------------------------
 Symbol           Meaning
 ------------------------------------------
 A        Alanine
 B        Aspartic Acid, Asparagine
 C        Cystine
 D        Aspartic Acid
 E        Glutamic Acid
 F        Phenylalanine
 G        Glycine
 H        Histidine
 I        Isoleucine
 K        Lysine
 L        Leucine
 M        Methionine
 N        Asparagine
 P        Proline
 Q        Glutamine
 R        Arginine
 S        Serine
 T        Threonine
 V        Valine
 W        Tryptophan
 X        Unknown
 Y        Tyrosine
 Z        Glutamic Acid, Glutamine
 *        Terminator
 IUPAC-IUP AMINO ACID SYMBOLS:
   Biochem J. 1984 Apr 15; 219(2): 345-373
   Eur J Biochem. 1993 Apr 1; 213(1): 2

ACKNOWLEDGEMENTS
Bioperl owes its early organizational support to its association with the award-winning VSNS-BCD BioComputing Courses; some students of the 1996 course (Chris Dagdigian, Richard Resnick, Lew Gramer, Alessandro Guffanti, and others) have contributed code and commentary. Georg Fuellen, the VSNS-BCD chief organizer was one of the early driving forces behind bioperl. Steven Brenner, who was an early adopter of Perl for bioinformatics provided some of the early work on bioperl. Lincoln Stein has long provided guidance and code.

Bioperl was then taken up by people developing code at the large genome centres. In particular at Stanford, Steve Chervitz at the Genome Sequencing Centre (St Louis) Ian Korf and at the Sanger Centre (Cambridge UK) Ewan Birney. All of the C code XS extensions were provided by Ewan Birney. Bioperl is used in anger at these sites, indicating that is both useful and that it works.

Jason Staijch and Hilmar Lapp joined bioperl for the drive towards a 0.7 release over 2000 and the first part of 2001, which includes a revised feature location model, richer feature objects (in particular genes) and more and better tools. Peter Schatner and Lorenz Pollak contributed serious chunks of code, being the AlignIO and bptutorial scripts and the BPLite port to bioperl respectively. At this time Bioperl was being used in absolute earnest by the Ensembl group which shook out a number of problems in the code base. Additional compatibility with the Sequence Workbench (bioperl-gui) (Mark Wilkinson and David Block) and Biocorba (Jason Staijch, Brad Chapman and Alan Robinson) and finally Game-XML (Brad Marshall) provided more interoperability.

Current server hardware for bioperl.org (and other open-bio.org hosted projects) was provided by Compaq Computer Corporation. The donation was facilitated by both the Pharmaceutical Sales and High Performance Technical Computing (HPTC) groups.

The bioperl servers reside in Cambridge, Massachusetts USA with colocation facilities and internet bandwidth donated by Genetics Institute. In particular Dr. Steven Howes, Kenny Grant & Rich DiNunno have made significant efforts on our behalf.

COPYRIGHT
 Copyright (c) 1996-2000 Georg Fuellen, Richard Resnick, Steven E. Brenner,
 Chris Dagdigian, Steve A. Chervitz, Ewan Birney, James Gilbert, Elia Stupka,
 and others. All Rights Reserved. This module is free software;
 you can redistribute it and/or modify it under the same terms as Perl itself.