Class Specialization

Pam

Pam scoring matrices.

Pam |

Parameters

Type of the score values. Default: | |

Type of alphabet underlying the matrix. Default: | |

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: Default: |

Specialization of

Functions

Given a multiple alignment, this function calculates all kinds of alignment statistics. (Score) | |

Coordinates computation by invokating extrapolation, alphabet extension, rounding, scaling, type conversion and symmetrization. | |

returns the distance on which PAM matrix computation is based. | |

returns entropy of the PAM matrix. | |

Access function returning the distance dependent | |

Computes the best global alignment of the two sequences. (Score) | |

Computes the best local alignment of two sequences. (Score) | |

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. 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) | |

Computes multiple local alignments of two sequences. (Score) | |

The score for aligning two values according to a scoring scheme. | |

Score for extending gaps. | |

Score for opening a gap. | |

Computes the best local alignment of the (two) sequences given in align. (Score) | |

Computes next best local alignment. (Score) | |

Given 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.

Example Programs

SeqAn - Sequence Analysis Library - www.seqan.de