score_alignment: Score a simple alignment

In brouwern/compbio4all: Datasets and helpful functions for learning bioinformatics and computational biology

Description

Score a simple alignment

Usage

score_alignment(
  seq.df,
  seq1,
  seq2,
  sub.mat,
  gap.penalty = -10,
  gap.extend = -4
)

Arguments

seq.df	Two aligned sequences in a dataframe
seq1	name of column with first sequences
seq2	name of column with second sequence
sub.mat	substitution matrix to use. Defaults to BLOSUM62
gap.penalty	penalty for gaps in the sequence
gap.extend	penalty for gap length, starting with the first gap.

brouwern/compbio4all documentation built on Dec. 19, 2021, 11:47 a.m.