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mac multiple sequence alignment

JMILLER%VXBIO.SPAN at STAR.STANFORD.EDU JMILLER%VXBIO.SPAN at STAR.STANFORD.EDU
Sat Aug 18 19:14:56 EST 1990


  To answer Jay Zuccola's request;
  Multiple sequence alignment on the mac is a big problem, since none
of the programmers who write these programs write for the mac. Thus,
any program will be a port, and I am apparently the only person who has
done this. I ported THREE from Russell Doolittle's lab in 1987. It has
obvious problems when the sequences don't start at about the same place.
More recently, I produced a mac version of CLUSTAL, which can align
both DNA and protein sequences. It required a MacII and 3megs memory for
reasonable performance. Unfortunately, IntelliGenetics owns the rights 
to this program, so I can't distribute it. I sent the source code for
the port to Chris Dow last spring, so mabye all or part of CLUSTAL will
appear in the Mac sequence analysis program they have developed.
 I also have gotten Russell Doolittle's package to 'run' on the mac.
This package includes programs like PRELAIGN,TREE,SCORE, etc. It does
a good job of alignment. Unfortunately, there are some subtle compiler
differences between MPW C and the unix compiler used for the programs,
which has introduced bugs I haven't been able to fix. The programs
demand >4 megs RAM, even though they should run in about 2.5 megs, and
have random,sequence-dependent crashes. I have sent the source to a
programmer friend of mine, Carl Lawyer, to see if HE can figure out
the problem. If and when these programs are fixed, they will be avaialble
for free.
 That's all I know. Since so many people have macs these days, it would
be nice to have a program of this type. I don't have the time to write
one from scratch. If anyone out there is interested in either (1)writing
a multiple sequence alignment program for the mac, or (2)porting their
software to the mac, they are welcome to contact me about the whys and
wherefores.
 -Peter Markiewicz




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