testalign-methods {pairseqsim}R Documentation

Scoring of optimal alingments.

Description

Computes optimal pairwise alignment of 2 protein sequences. For internal use.

Arguments

obj1 see above
obj2 see above
sub Substitution matrix
delta gap opening penalty
gapext gap extension penalty
alignment type of alignment: c("global","local","overlap")
scoring type of scoring, identity, similarity, score, scoreN, pozitive

Value

For two objects of class AASequence returns an object of class AAAlignment.\ Otherwise it returns a score. If used with NULL as second parameter it returns a distance matrix. The scores are transformed into distances. For details see the vignette.

Methods

obj1 = "AASequence", obj2 = "AASequence"
Computes obtimal alignment of two sequences and returns score.

Author(s)

Witold E. Wolski


[Package pairseqsim version 1.0.4 Index]