Search results for "dist:BioPerl Bio::Matrix::PSM::PsmI"
Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies
Supposed to handle a combination of site matrices and/or their corresponding sequence matches (instances). This object inherits from Bio::Matrix::PSM::SiteMatrix, so you can use the respective methods. It may hold also an array of Bio::Matrix::PSM::I...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file
Generally you should not use this object directly, you can access the information through a PSM driver (See Bio::Matrix::PSM::IO). It is handling the header data from a PSM file which may be very different. This means that some of the methods will re...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Matrix::PSM::SiteMatrixI - 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::InstanceSiteI - InstanceSite interface, holds an instance of a PSM
Abstract interface to PSM site occurrence (PSM sequence match). InstanceSite objects may be used to describe a PSM (See Bio::Matrix::PSM::SiteMatrix) sequence matches. The usual characteristic of such a match is sequence coordinates, score, sequence ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Matrix::PSM::IO - PSM parser
This module allows you to read DNA position scoring matrices and/or their respective sequence matches from a file. There are two header methods, one belonging to Bio::Matrix::PSM::IO::driver and the other to Bio::Matrix::PSM::Psm. They provide genera...
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
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