> FIRST QUESTION: > SECOND QUESTION: A bit of a plug, but you might want to look at the Bioconductor project (www.bioconductor.org), which has a variety of packages that will handle the situations you are looking for. Depending on exactly what you're looking to do, the annotate, AnnBuilder and SAGElyzer packages might be up your alley. Note that every package (well, almost every package) has several task-specific documents, available here: http://www.bioconductor.org/viglistingindex.html It might be worthwhile checking some of those out (again, I suspect that the three packages mentioned above might be what you'd want to target). There's also a mailing list (linked off the website) if you're interested in knowing more. -J