Class Specialization
Pam
Pam scoring matrices.
Score<TValue, Pam<TSequenceValue, TSpec> >
Parameters
TValue
Type of the score values.
Default: int
TSequenceValue
Type of alphabet underlying the matrix.
Default: AminoAcid
TSpec
Origin of starting data underlying the pam matrix computation. The starting data are the mutation probability matrix and the frequencies of occurence of each identifier.
Values: Pam_Data_Dayhoff_MDM78, Pam_Data_Jones_PRI29, Pam_Data_Jones_PET91_SWISS15, Pam_Data_Jones_PET91_SWISS22, Pam_Data_Jones_All_Membrane, Pam_Data_Jones_Single_Membrane, Pam_Data_Jones_Multi_Membrane
Default: Pam_Data_Dayhoff_MDM78
Specialization of
Functions
alignmentEvaluationGiven a multiple alignment, this function calculates all kinds of alignment statistics. (Score)
buildPamCoordinates computation by invokating extrapolation, alphabet extension, rounding, scaling, type conversion and symmetrization.
getDistreturns the distance on which PAM matrix computation is based.
getEntropyreturns entropy of the PAM matrix.
getScaleAccess function returning the distance dependent scaling factor used for PAM matrix computation
globalAlignmentComputes the best global alignment of the two sequences. (Score)
localAlignmentComputes the best local alignment of two sequences. (Score)
matchRefinementRefines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping. (Score)
multiLocalAlignmentComputes multiple local alignments of two sequences. (Score)
scoreThe score for aligning two values according to a scoring scheme.
scoreGapExtendScore for extending gaps.
scoreGapOpenScore for opening a gap.
smithWatermanComputes the best local alignment of the (two) sequences given in align. (Score)
smithWatermanGetNextComputes next best local alignment. (Score)
sumOfPairsScoreGiven a multiple alignment, this function calculates the sum-of-pairs score. (Score)
Remarks
This class computes pam matrices for arbitrary alphabets and starting values. The computation precedure includes extrapolation of the MDM (Mutation Probability Matrix) to the desired evolutionary distance in units of 1 PAM, computation of the odds scores and the construction of the symmetric and scaled logarithms of odds matrix. The odds scores thereby represent the chance of a relationship between the observed amino acids at each position versus the chance of coincidental pairing. If integer scores are produced, each value is rounded separately.
SeqAn - Sequence Analysis Library - www.seqan.de