Search results for "dist:BioPerl Bio::Symbol::Alphabet"
Bio::Tools::IUPAC - Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence
Bio::Tools::IUPAC is a tool that manipulates sequences with ambiguous residues following the IUPAC conventions. Non-standard characters have the meaning described below: IUPAC-IUB SYMBOLS FOR NUCLEOTIDE (DNA OR RNA) NOMENCLATURE: Cornish-Bowden (1985...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SimpleAlign - Multiple alignments held as a set of sequences
SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipula...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::SeqPattern - represent a sequence pattern or motif
Bio::Tools::SeqPattern module encapsulates generic data and methods for manipulating regular expressions describing nucleic or amino acid sequence patterns (a.k.a, "motifs"), such as the ones produced by Bio::Tools::IUPAC. Bio::Tools::SeqPattern is a...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment
This object contains routines for calculating various statistics and distances for DNA alignments. The routines are not well tested and do contain errors at this point. Work is underway to correct them, but do not expect this code to give you the rig...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Matrix::PSM::SiteMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
SiteMatrix is designed to provide some basic methods when working with position scoring (weight) matrices, such as transcription factor binding sites for example. A DNA PSM consists of four vectors with frequencies {A,C,G,T}. This is the minimum info...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Matrix::PSM::ProtMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.
ProtMatrix is designed to provide some basic methods when working with position scoring (weight) matrices related to protein sequences. A protein PSM consists of 20 vectors with 20 frequencies (one per amino acid per position). This is the minimum in...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC