Bio::Prospect::File - interface to Prospect Files River stage zero No dependents

Bio::Prospect::File is a subclass of IO::File and is intended for use for parsing Prospect XML files. It is used by Bio::Prospect::LocalClient to return Thread objects from Prospect output....

REECE/Bio-Prospect-1.04 - 19 Nov 2003 06:34:27 UTC - Search in distribution

Bio::Tools::Prepeat - Finding repeats in protein sequences River stage zero No dependents

This is a module for locating repeats in protein sequences. Usage is as follows: feed the sequences, build index files, perform queries, and then it will return a reference to the repeat data....

XERN/Bio-Tools-Prepeat-0.06 - 07 May 2003 20:17:42 UTC - Search in distribution

Bio::Affymetrix::CHP River stage zero No dependents

The Affymetrix microarray system produces files in a variety of formats. If this means nothing to you, these modules are probably not for you :). This module parses CHP files. This module requires a Bio::Affymetrix::CDF object before it can do anythi...

SKIPPY/Bio-Affymetrix-0.5 - 21 Jul 2005 11:48:59 UTC - Search in distribution

Bio::Align::Graphics - Graphic Rendering of Bio::Align::AlignI Objects River stage one • 1 direct dependent • 1 total dependent

Bio::Align::Graphics is a module designed to create image files out of Bio::Align::AlignI objects. An alignment may be manipulated with various formatting and highlighting options. An example: #!/usr/bin/perl -w use Bio::AlignIO; use Bio::Align::Grap...

CJFIELDS/Bio-Align-Graphics-1.7.3 - 25 Sep 2018 00:17:21 UTC - Search in distribution

Bio::BLAST::Database - work with formatted BLAST databases River stage one • 1 direct dependent • 1 total dependent

Each object of this class represents an NCBI-formatted sequence database on disk, which is a set of files, the exact structure of which varies a bit with the type and size of the sequence set. This is mostly an object-oriented wrapper for using NCBI'...

RBUELS/Bio-BLAST-0.4 - 12 Sep 2011 15:47:19 UTC - Search in distribution

Bio::ConnectDots::DB - Database adapter for 'connect-the-dots' River stage zero No dependents

This class manages database connections and encapsulates all database access for 'connect-the-dots'....

DBURDICK/Bio-ConnectDots-1.0.2 - 07 Apr 2005 22:06:44 UTC - Search in distribution

Bio::DNA::Incomplete - Match incompletely specified bases in nucleic acid sequences River stage zero No dependents

Sometimes DNA patterns are given with incomplete nucleotides that match more than one real nucleotide. This module helps you deal with them....

LEONT/Bio-DNA-Incomplete-0.004 - 01 Oct 2013 12:23:59 UTC - Search in distribution

Bio::Draw::Pictogram - generate SVG output of Pictogram display for consensus motifs River stage zero No dependents

A module for generating SVG output of Pictogram display for consensus motifs. This method of representation was describe by Burge and colleagues: (Burge, C.B.,Tuschl, T., Sharp, P.A. in The RNA world II, 525-560, CSHL press, 1999) This is a simple mo...

CJFIELDS/Bio-Draw-Pictogram-1.7.3 - 25 Sep 2018 01:19:29 UTC - Search in distribution

Bio::MAGE::SQLWriter - a module for exporting MAGE-OM objects to a database River stage zero No dependents

Methods for transforming information from a MAGE-OM objects into tuples in a MAGE database....

JASONS/Bio-MAGE-Utils-20030502.0 - 14 May 2007 10:52:47 UTC - Search in distribution

Bio::Index::Stockholm - Interface for indexing Stockholm files River stage one • 1 direct dependent • 1 total dependent

Indexes Stockholm format alignments such as those from Pfam and Rfam. Returns raw stream data using the ID or a Bio::SimpleAlign object (via Bio::AlignIO). This module also allows for ID parsing using a callback: $inx->id_parser(\&get_id); # make the...

CJFIELDS/Bio-AlignIO-stockholm-1.7.3 - 25 Sep 2018 00:14:27 UTC - Search in distribution

Bio::MUST::Apps::Leel - Main class for leel tool River stage one • 1 direct dependent • 1 total dependent

# TODO...

DBAURAIN/Bio-MUST-Apps-FortyTwo-0.202160 - 03 Aug 2020 18:14:09 UTC - Search in distribution


Bio::SAGE::Comparison - Compares data from serial analysis of gene expression (SAGE) libraries. River stage zero No dependents

This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE) libraries....

SCOTTZED/Bio-SAGE-Comparison-1.00 - 25 May 2004 01:40:01 UTC - Search in distribution

Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output River stage zero No dependents

This outputs a tree as an SVG graphic using the SVG::Graph API...

CJFIELDS/Bio-TreeIO-svggraph-1.7.3 - 25 Sep 2018 01:27:35 UTC - Search in distribution

App::RecordStream::Bio - A collection of record-handling tools related to biology River stage zero No dependents

App::RecordStream::Bio is a collection of record-handling tools related to biology built upon the excellent App::RecordStream. The operations themselves are written as classes, but you'll almost always use them via their command line wrappers within ...

TSIBLEY/App-RecordStream-Bio-0.24 - 04 Aug 2017 17:45:08 UTC - Search in distribution

Bio::Tools::Run::QCons - Run Qcons to analyze protein-protein contacts River stage zero No dependents

This module implements a wrapper for the QCons application. QCons itself is an implementation of the Polyhedra algorithm for the prediction of protein-protein contacts. From the program's web page (<http://tsailab.tamu.edu/QCons/>): "QContacts allows...

BRUNOV/Bio-Tools-Run-Qcons-0.112881 - 15 Oct 2011 21:39:17 UTC - Search in distribution

Bio::Draw::FeatureStack - BioPerl module to generate GD images of stacked gene models River stage zero No dependents

FeatureStack creates GD images of vertically stacked gene models to facilitate visual comparison of gene structures. Compared genes can be clusters of orthologous genes, gene family members, or any other genes of interest. FeatureStack takes an array...

CHRISFR/Bio-Draw-FeatureStack-0.03 - 29 Jun 2012 21:09:13 UTC - Search in distribution

Bio::GMOD::Blast::Graph - display a graphical summary of a BLAST report River stage one • 1 direct dependent • 1 total dependent

This package provides methods for graphically displaying a BLAST search report....

RBUELS/Bio-GMOD-Blast-Graph-0.06 - 10 Aug 2011 21:10:47 UTC - Search in distribution

Bio::MUST::Apps::OmpaPa - Main class for ompa-pa tool River stage zero No dependents

# TODO...

DBAURAIN/Bio-MUST-Apps-OmpaPa-0.201810 - 29 Jun 2020 08:28:32 UTC - Search in distribution

Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing. River stage zero No dependents

This object implements a NCBI Blast XML parser. It requires XML::SAX; it is also recommended (for faster parsing) that XML::SAX::ExpatXS or XML::LibXML be installed. Either 'XML::SAX::ExpatXS' or 'XML::LibXML::SAX::Parser' should be set as the defaul...

CJFIELDS/Bio-SearchIO-blastxml-1.70 - 04 Jan 2018 02:12:33 UTC - Search in distribution

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