9.5 Overview of Objects

Bioperl is a big project and a fairly large collection of modules. Some of these modules are standalone; others interact with each other in various ways.

Your first task in learning about Bioperl is to get an idea of the main subject areas the modules are designed to address. So to begin with, here is a brief overview of the main types of objects in Bioperl, collected in a few broadly defined groups.

Sequences

Bio::Seq is the main sequence object in Bioperl.

Bio::PrimarySeq is a sequence object without features.

Bio::SeqIO provides sequence file input and output.

Bio::Tools::SeqStats provides statistics on a sequence.

Bio::LiveSeq::* handles changing sequences.

Bio::Seq::LargeSeq provides support for very large sequences.

Databases

Bio::DB::GenBank provides GenBank access. Similar modules are available for several biological databases.

Bio::Index::* indexing and accessing local databases.

Bio::Tools::Run::StandAloneBlast runs BLAST on your local computer.

Bio::Tools::Run::RemoteBlast runs BLAST remotely.

Bio::Tools::BPlite parses BLAST reports .

Bio::Tools::BPpsilite parses psiblast reports.

Bio::Tools::HMMER::Results parses HMMER hidden Markov model results.

Alignments

Bio::SimpleAlign manipulates and displays simple multiple sequence alignments.

Bio::UnivAln manipulates and displays multiple sequence alignments.

Bio::LocatableSeq are sequence objects with start and end points for locating relative to other sequences or alignments.

Bio::Tools::pSW aligns two sequences with the Smith-Waterman algorithm.

Bio::Tools::BPbl2seq is a lightweight BLAST parser for pairwise sequence alignment using the BLAST algorithm.

Bio::AlignIO also aligns two sequences with BLAST.

Bio::Clustalw is an interface to the Clustalw multiple sequence alignment package.

Bio::TCoffee is an interface to the TCoffee multiple sequence alignment package.

Bio::Variation::Allele handles sets of alleles.

Bio::Variation::SeqDiff handles sets of mutations and variants.

Features and genes on sequences

Bio::SeqFeature is the sequence feature object in Bioperl.

Bio::Tools::RestrictionEnzyme locates restriction sites in sequence.

Bio::Tools::Sigcleave finds amino acid cleavage sites.

Bio::Tools::OddCodes rewrites amino acid sequences in abbreviated codes for specific statistical analysis (e.g., a hydrophobic/hydrophilic two-letter alphabet).

Bio::Tools::SeqPattern provides support for regular expression descriptions of sequence patterns.

Bio::LocationI provides an interface to location information for a sequence.

Bio::Location::Simple handles simple location information for a sequence, both as a single location and as a range.

Bio::Location::Split provides location information where the location may encompass multiple ranges, and even multiple sequences.

Bio::Location::Fuzzy provides location information that may be inexact .

Bio::Tools::Genscan is an interface to the gene finding program.

Bio::Tools::Sim4::Results (and Exon) is an interface to the gene exon finding program.

Bio::Tools::ESTScan is an interface to the gene finding program.

Bio::Tools::MZEF is an interface to the gene finding program.

Bio::Tools::Grail is an interface to the gene finding program.

Bio::Tools::Genemark is an interface to the gene finding program.

Bio::Tools::EPCR parses the output of ePCR program.