sequence alignment

jmiller at vxbio.DNET.NASA.GOV jmiller at vxbio.DNET.NASA.GOV
Wed Sep 25 11:37:19 EST 1991


 Currently, there are a couple of sequence alignment programs. I assume
that when you say "sequence alignment" you are referring to aligning 
several sequences ALREADY known to be homologous to each other, rather
than searching a database for sequences homologous to your query sequence.
  1.THREE-old port of program written in Russell Doolittle's lab, aligns
    3 protein sequences ONLY of they share homologous amino terminal
    regions.
  2.CLUSTALV aligns DNA and protein sequences, tree-building, complete
    rewrite of older program available on VAX. Doesn't use a mac user
    interface, but gets the job done.
  3.Doolittle's progressive alignment package. For proteins only. Uses
    several programs to progressively align sequences. Will be available
    shortly.
Note that ALL multiple sequence alignment programs require huge amounts
of RAM, and most require you use a MacII with a 68020 and math coprocessor.
A Mac Plus or SE won't work. Typical configuration required is a mac II
with coprocessor (the LC doesn't have one by default), and 4-5megs RAM.
This isn't a restriction likely to be lifted in the future.

-Peter Markiewicz




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