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.

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 bio.perl.org (http://bio.perl.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 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.

OBJECTS

Sequence objects

Bio::Seq Sequence object

This module is the generic sequence object which lies at the core of the bioperl project. It stores DNA, RNA, or amino acid sequence information and brief annotation. It has associated methods to perform various manipulations of sequences and support for a reading and writing sequence data in a variety of file formats.

Seq.pm has its own detailed documentation.

Blast objects

Bio::Tools::Blast

The Bio::Tools::Blast.pm module encapsulates data and methods for running, parsing, and analyzing pre-existing BLAST reports.

Blast.pm and all associated helper modules all have their own detailed documentation.

FEATURES:

       o Supports NCBI Blast1.x, Blast2.x, and WashU-Blast2.x,
         gapped and ungapped. Can parse HTML-formatted as well 
         as non-HTML-formatted reports.

       o Launch new Blast analyses remotely or locally.
         Blast objects can be constructed directly from the
         results of the run.  (Support for local Blasts 
         is not yet complete.)

       o Construct Blast objects from pre-existing files or from
         a new run.
         Build a Blast object from a single file or build
         multiple Blast objects from an input stream containing
         multiple reports. 

       o Add hypertext links from a BLAST report.

       o Generate sequence and sequence alignment objects from
         HSP sequences.

Restriction Enzyme objects

Bio::Tools::RestrictionEnzyme

The Bio::Tools::RestrictionEnzyme.pm module encapsulates generic data and methods for using restriction endonucleases for in silico restriction analysis of DNA sequences.

RestrictionEnzyme.pm has its own detailed documentation.

Protein Smith-Waterman alignment objects

Bio::Tools::pSW

This module allows the production of Smith Waterman alignments. Warning it requires a compiled-C extension (bp_sw) which is provided in the distribution. The Bio::Tools::pSW object is an object factory which builds Bio::SimpleAlign objects from two protein sequences objects (Bio::Seq).

DNA alignments will be added soon.

SimpleAlign objects

Bio::SimpleAlign

Bio::SimpleAlign encapsulates multiple alignments as simple blocks of immutable sequences. This modules provides principly I/O of multiple alignments and some easy ways to iterate over an alignment

It is not capable of complex join or editing functions, which is better provided by Georg Fuellen's UnivAln module. Nor does it make alignments, which must be done by external programs or, for pairwise alignments, the Bio::Tools::pSW module

Other Modules

(** to be completed **)

Using the Bio::Root modules with your own perl5 classes

The example directory in the bioperl distribution examples/root_object/ contains code and scripts that show how the Bio::Root modules can be used as a foundation for robust and fault tolerant perl5 classes.

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 heirarchy. See http://bio.perl.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 vsns-bcd-perl-guts@lists.uni-bielefeld.de (the bioperl 'guts' 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://bio.perl.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@bio.perl.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 'guts' mailing list vsns-bcd-perl-guts@lists.uni-bielefeld.de

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

TODO

There are many many aspects of bioperl that are being worked on or should be worked on. Below lists a non exhaustive set: it is very likely by the time you read this document that some of these things have been done already, so check out http://bio.perl.org for more details. Some modules have their own TODO section, which will contain module- specific action items.

Documentation clean-up

'Meta' documentation is still spread around the different objects rather than in here

Bio::Structure

A number of people have been talking about a Structure object (probably an object heirarchy). See http://bio.perl.org/Projects/Structure for the current state-of-affairs in this area and to learn how to get involved.

Perl version support

All modules included in the intial Bioperl distribution support 5.003 and higher. At some point we will begin adding features and modules that require later versions of perl. Individual modules perhaps should explicitly impose their own perl version requirements. Consider this issue open for discussion on the guts (developer) mailing list.

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 is one of the driving forces behind bioperl. Steve Brenner, who was an early adopter of Perl for bioinformatics provided some of the early work on bioperl.

Bioperl was then taken up by people developing code at the large genome centres. In particular at Stanford, Steve Chervitz (the current bioperl coordinator), 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.

Uni-bielefeld provides us with our Mailing lists.

Jon Orwant at The Perl Journal (http://www.tpj.com) gave us permission to reprint Lincoln Stein's great article on our website. He also worked with the Perl Institute (http://www.perl.org) to arrange our perl.org DNS entry.

Hardware for bio.perl.org was donated by Compaq.

Bandwith and internet connectivity (ISDN) donated by The Genetics Institute (http://www.genetics.com).

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.