Search results for "Bio::Structure::Model"
Bio::Genex::ControlledVocab - Methods for processing data from the GeneX DB table: ControlledVocab
Each Genex class has a one to one correspondence with a GeneX DB table of the same name (*i.e.* the corresponding table for Bio::Genex::ControlledVocab is ControlledVocab). Most applications will first create an instance of Bio::Genex::ControlledVoca...
JASONS/Bio-Genex-2.6.0 - 06 Feb 2001 23:15:15 UTC - Search in distribution
GD::SVG - Seamlessly enable SVG output from scripts written using GD
GD::SVG painlessly enables scripts that utilize GD to export scalable vector graphics (SVG). It accomplishes this task by wrapping SVG.pm with GD-styled method calls. To enable this functionality, one need only change the "use GD" call to "use GD::SV...
TWH/GD-SVG-0.33 - 10 May 2009 14:39:31 UTC - Search in distribution
HackaMol - HackaMol: Object-Oriented Library for Molecular Hacking
The HackaMol publication <http://pubs.acs.org/doi/abs/10.1021/ci500359e> has a more complete description of the library (pdf available from researchgate <http://www.researchgate.net/profile/Demian_Riccardi/publication/2737781 91_HackaMol_an_object-or...
DEMIAN/HackaMol-0.053 - 23 Feb 2022 00:55:44 UTC - Search in distribution
go-perl - perl modules for GO and other OBO ontologies
go-perl is part of the go-dev code distribution. It is also available as a seperate library in its own right. go-perl is a collection of perl modules for working with ontologies and data, in particular the Gene Ontology and other Open Bio-Ontologies....
CMUNGALL/go-perl-0.15 - 12 Jun 2013 16:22:41 UTC - Search in distribution- GO::Parser - parses all GO files formats and types
Bio::Trace::ABIF - Perl extension for reading and parsing ABIF (Applied Biosystems, Inc. Format) files
VITA/Bio-Trace-ABIF-1.06
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02 Nov 2016 11:16:32 UTC
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Bio::NEXUS
This User Manual explains the motivation for developing the Bio::NEXUS library, the principles underlying its organization, and its use in developing software for evolutionary informatics. This manual also provides information on how to use two demon...
ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 UTC - Search in distribution
Bio::App::SELEX::RNAmotifAnalysis - Cluster SELEX sequences and calculate their structures
This module pipelines steps in the analysis of SELEX (Systematic Evolution of Ligands through EXponential enrichment) data. This main module creates scripts to do the following: (1) Cluster similar sequences based on edit distance. (2) Align sequence...
MOLECULES/Bio-App-SELEX-RNAmotifAnalysis-0.0095 - 10 Apr 2014 14:22:57 UTC - Search in distribution- Bio::App::SELEX::RNAmotifAnalysis - Cluster SELEX sequences and calculate their structures
Bio::Homology::InterologWalk - Retrieve, prioritise and visualize putative Protein-Protein Interactions through interolog mapping
A common activity in computational biology is to mine protein-protein interactions from publicly available databases to build *Protein-Protein Interaction* (PPI) datasets. In many instances, however, the number of experimentally obtained annotated PP...
GGALLONE/Bio-Homology-InterologWalk-0.58 - 01 Feb 2012 12:31:34 UTC - Search in distribution
Chemistry::File::PDB - Protein Data Bank file format reader/writer
This module reads and writes PDB files. The PDB file format is commonly used to describe proteins, particularly those stored in the Protein Data Bank (<http://www.rcsb.org/pdb/>). The current version of this module only reads the following record typ...
ITUB/Chemistry-File-PDB-0.23 - 10 May 2009 21:58:55 UTC - Search in distribution
Bio::Prospect::Thread - Representation of a Prospect thread.
Bio::Prospect::Thread -- Representation of a full Prospect thread this is really just a set of methods associated with the hash structure returned by XML::Simple....
REECE/Bio-Prospect-1.04 - 19 Nov 2003 06:34:27 UTC - Search in distribution
Bio::Chaos::ChaosGraph - object for representing a chaos-xml dataset
This class allows manipulation of in-memory Chaos documents as Data::Stag nodes, and provides additional methods for traversing the graph structure defined in the Chaos document...
CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC - Search in distribution
Bio::Draw::FeatureStack - BioPerl module to generate GD images of stacked gene models
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::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair
This implementation is "Generic", meaning it is is suitable for holding information about High Scoring pairs from most Search reports such as BLAST and FastA. Specialized objects can be derived from this. Unless you're writing a parser, you won't eve...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::SearchIO::infernal - SearchIO-based Infernal parser
- Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser
- Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
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Bio::Phylo::Matrices::MatrixRole - Extra behaviours for a character state matrix
This module defines a container object that holds Bio::Phylo::Matrices::Datum objects. The matrix object inherits from Bio::Phylo::Listable, so the methods defined there apply here....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC - Search in distribution- Bio::Phylo::EvolutionaryModels - Evolutionary models for phylogenetic trees and methods to sample these Klaas Hartmann, September 2007
- Bio::Phylo::NeXML::DOM - XML DOM support for Bio::Phylo
Bio::ToolBox::SeqFeature - Fast, simple SeqFeature implementation
SeqFeature objects represent functional elements on a genomic or chromosomal sequence, such as genes, transcripts, exons, etc. In many cases, especially genes, they have a hierarchical structure, typically in this order gene mRNA or transcript exon C...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution
Bio::PDB::Structure::Atom - Perl module for parsing and manipulating Protein Databank (PDB) files
This module combines tools that are commonly used to analyze proteins and nucleic acids from a pdb file stuctures. The main benefits of using the module are its ability to parse and print out a pdb structure with minimum effort. However in addition t...
RULIX/Bio-PDB-Structure-0.02 - 22 Jul 2012 15:49:40 UTC - Search in distribution
Bio::Tools::Run::Phylo::Phylip::SeqBoot - Wrapper for the phylip program SeqBoot
Wrapper for seqboot from the phylip package by Joseph Felsentein. Taken from phylip doc... "SEQBOOT is a general boostrapping tool. It is intended to allow you to generate multiple data sets that are resampled versions of the input data set. SEQBOOT ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution
FAST::Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
Most GenBank entries for annotated genomic DNA contain a flat list of features. These features can be parsed into an equivalent flat list of FAST::Bio::SeqFeatureI objects using the standard FAST::Bio::SeqIO classes. However, it is often desirable to...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::SearchIO::infernal - SearchIO-based Infernal parser
- FAST::Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser