| Class Specialization Pam Pam scoring matrices.
Score
Pam
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 Score Functions
buildPam | Coordinates computation by invokating extrapolation, alphabet extension, rounding, scaling, type conversion and symmetrization.
getDist | returns the distance on which PAM matrix computation is based.
getEntropy | returns entropy of the PAM matrix.
getScale | Access function returning the distance dependent scaling factor used for PAM matrix computation
globalAlignment | Computes the best global alignment of the two sequences. (Score)
localAlignment | Computes the best local alignment of two sequences. (Score)
matchRefinement | Refines (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)
score | The score for aligning two values according to a scoring scheme.
scoreGapExtend | Score for extending gaps.
scoreGapOpen | Score for opening a gap.
smithWaterman | Computes the best local alignment of the (two) sequences given in align. (Score)
smithWatermanGetNext | Computes next best local alignment. (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. Example Programs Global Alignments, Local Alignments SeqAn - Sequence Analysis Library - www.seqan.de