http://argital.cz/?kozka=katolick%C3%BD-t%C3%BDden%C3%ADk-seznamka&347=a6 matchPWM() is now part of Biostrings 2.7.47 (in BioC devel, so you need R-2.7). Load Biostrings: library(Biostrings) Suppose ‘pwm’ contains a Position Weight Matrix, let’s say: pwm maxWeights(pwm) # the max weight in each column [1] 17 20 19 20 18 18 20 8 > maxScore(pwm) # the max possible score [1] 140 Let’s match…