In Bioconductor, Is it possible to create a PWM from DNA sequence alignment with gaps to be used to scan sequences? When I try it as suggested in "Biostrings" it gives the following error: > pwm <- PWM(pfm) Error in .normargPfm(x) : invalid PFM 'x': IUPAC ambiguity letters are represented The help for "PWM" does say "with no IUPAC ambiguity letters" and Gaps are ambiguity letters. > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Biostrings_2.28.0 IRanges_1.18.3 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] stats4_3.0.1 tools_3.0.1 -best -Lax [[alternative HTML version deleted]]