The guy at the computer on my left uses Sequencher; the gal
on the computer to my right uses PHRAP. Therefore I consider
myself an expert on both, although I use neither. The Mac has
a great user interface; if a program can run on it and take
advantage of the interface, that's great. DNA*'s Seqman and
Gene Code's Sequencher both do. Therefore they are good programs.
But PHRAP's algorithm is light years ahead. I've seen it
chew through data sets that leave the other algorithms in tangled
repeats. Next cosmid I assemble will be with PHRAP. My time is
just too valuable to waste on the extra contig editing I would have
to do with one of the Mac programs. If Phil puts out a version of
PHRAP for the Mac, the world will be a better place. Maybe now
that he has some potential income from commercail sales of PHRAP,
he will have the resources and will to do so. But I think it will
be a consuming job just keeping up the UNIX PHRAP. I don't think
we should expect a Mac PHRAP anytime soon.
That said, for very small data sets like might be accumulated
by sequence walking across a cDNA, one might as well use one of the
Mac programs.
------------------------------------------------------------------
Jared C. Roach
Department of Molecular Biotechnology
Health Sciences Building, Room K354
University of Washington
Box 357730
Seattle, WA 98195
phone (206) 616-4536
FAX (206) 685-7301
roach at u.washington.eduhttp://weber.u.washington.edu/~roach/
