Hi, How does it work with mismatch.min, mismatch.max in the functions of Biostrings for ex, vcountPattern? If mismatch.min=0, mismatch.max=2, then if there is no match, the function searches up to 2 matches, that is, if it find matches with 1mismatch, then it searches in the pattern in the next subject, otherwise it tries to find 2 matches in the same subject? Look forward to your reply, Carol [[alternative HTML version deleted]]

First, see ?`lowlevel-matching`, and if you are really adventurous, the function nedit_at() in Biostrings/src/lowlevel_matching.c. The degree to which your pattern and subjects disagree, in a sense dictated by your with.indels=FALSE and fixed=TRUE arguments, is determined first, although actually only up to your max.mismatch limit. Then that (modified) ?distance" is tested against your min.mismatch constraint, as it says here: ?isMatchingAt?: If ?subject? is an XString object, then return the logical vector defined by: min.mismatch <= neditAt(...) <= max.mismatch On Jul 7, 2014, at 4:37 AM, carol white <wht_crl at="" yahoo.com=""> wrote: > Hi, > How does it work with mismatch.min, mismatch.max in the functions of Biostrings for ex, vcountPattern? If mismatch.min=0, mismatch.max=2, then if there is no match, the function searches up to 2 matches, that is, if it find matches with 1mismatch, then it searches in the pattern in the next subject, otherwise it tries to find 2 matches in the same subject? > > Look forward to your reply, > > Carol > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor