Structure Mismatch Score {R4RNA} | R Documentation |
Calculates a score that indicates how badly a set of basepairs (i.e. a secondary structure) fits with a sequence. A perfect fit is a structure where all basepairs form valid basepairs (A:U, G:C, G:U, and equivalents) and has a score of 0. Each basepair that forms a non-canonical pairing or pairs to gaps increases the score by 1, and each base-pair with a single-sided gap increases the score by 2.
structureMismatchScore(msa, helix, one.gap.penalty = 2, two.gap.penalty = 2, invalid.penalty = 1)
msa |
A multiple sequence alignment. Can be either a |
helix |
A helix data.frame |
one.gap.penalty |
Penalty score for basepairs with one of the bases being a gap |
two.gap.penalty |
Penalty score for basepairs with both bases being a gaps |
invalid.penalty |
Penalty score for non-canonical basepairs |
Returns an array of mismatch scores.
Jeff Proctor, Daniel Lai
data(helix) mismatch <- structureMismatchScore(fasta, known) # Sort by increasing mismatch sorted_fasta <- fasta[order(mismatch)]