substitution

A dataset containing several popular substitution scoring matrices
for DNA and amino acids.

datasets

Designed for the development and application of
hidden Markov models and profile HMMs for biological sequence analysis.
Contains functions for multiple and pairwise sequence alignment,
model construction and parameter optimization, file import/export,
implementation of the forward, backward and Viterbi algorithms for
conditional sequence probabilities, tree-based sequence weighting,
and sequence simulation.
Features a wide variety of potential applications including
database searching, gene-finding and annotation, phylogenetic
analysis and sequence classification.
Based on the models and algorithms described in Durbin et
al (1998, ISBN: 9780521629713).

Shaun Wilkinson

aphid

Analysis with Profile Hidden Markov Models

substitution function

A list of 71 matrices, most of which have 24 rows and 24 columns
corresponding to the 20-letter amino acid alphabet plus the ambiguity codes B, Z,
X and *:<dl>
 <dt>PAM</dt>
<dd>the PAM matrices from PAM10 to PAM500.</dd> <dt>BLOSUM</dt>
<dd>the BLOSUM matrices from BLOSUM30 to BLOSUM100.</dd> <dt>others</dt>
<dd>also included are the DAYHOFF, GONNET, IDENTITY
 and MATCH substitution matrices for amino acids,
 and the NUC.4.2 and NUC.4.4 substitution matrices for DNA.</dd>
</dl>

Format

Substitution matrices. — substitution

A list of 71 matrices, most of which have 24 rows and 24 columns
corresponding to the 20-letter amino acid alphabet plus the ambiguity codes B, Z,
X and *:<dl>
 <dt>PAM</dt>
<dd>the PAM matrices from PAM10 to PAM500.</dd>

 <dt>BLOSUM</dt>
<dd>the BLOSUM matrices from BLOSUM30 to BLOSUM100.</dd>

 <dt>others</dt>
<dd>also included are the DAYHOFF, GONNET, IDENTITY
 and MATCH substitution matrices for amino acids,
 and the NUC.4.2 and NUC.4.4 substitution matrices for DNA.</dd>


</dl>

substitution: Substitution matrices.

Description

Usage

Arguments

Format