I’ve received a lot of questions recently about TAMALg availability. Unfortunately, there is only a difficult-to-install package available right now; I sent it to someone recently and they had a terrible time getting it going.
I do describe the algorithm in the supplementary materials to the ENCODE spike-in competition paper (Johnson et al, Genome Research 2008).
I would love to have a simple package to distribute, but this is little supported in today’s granting environment; in fact, I don’t think that making algorithms widely available has ever been well-supported by any US funding agency. And I doubt the situation is different here in Canada.
I may be getting another undergrad soon and would task that person with working on the package. As a new faculty member, I am simply overwhelmed with basics like getting my lab going right now.
I do hope that this situation changes and thanks to all for patience.
As I have noted previously, the L2L3combo predictions produced by the TAMALPAIS server (see previous posts on this or just search for “TAMALPAIS Bieda” – no quotes, though) are the same predictions as made by TAMALg. TAMALg also adds the step of estimating enrichment via using maxfour type methodology.
So you can get good TAMALg predictions of sites just by using the webserver. I suggest going this route.
And to repeat – TAMALg is almost certainly NOT what you want for promoter arrays. Except if you have a factor in only a tiny fraction of promoters or one of the newer designs with very long promoter regions (e.g. for 10 kb promoters, might be ok).