In article <95048.140400LIU at QUCDN.QueensU.CA>, <LIU at QUCDN.QueensU.CA> wrote:
> Hello! Netters:
>> Would anyone know where I could FTP/Fetch/Gopher a Macintosh version
> DNA/protein sequence analysis program which allows me to get the actual
numbers
> (XX%) for the homology between two or more sequences? We have MacVector here.
> But it does not do it, instead it only aligns two sequences and I have to
> count the identical residues in order to get the numbers. Thanks!
>> Jian
> Jian Liu
> Department of Microbiology and Immunology
> Queen's University
> Kingston, Ontario K7L 3N6
>> Telephone# 613-545-6702
> Fax# 613-545-6796
> E-mail: LIU at QUCDN.QUEENSU.CA>> Mac Sequence Analysis Software
There are many others, I'm sure, but my HyperCard package will do
a % identity. Actually, I'm not sure I ever got around to doing
corrected (for multiple hits) distances but I really should.
Many of us would react to calling this % homology. Homology implies
similarity due to descent and you don't really know why the identity
is observed. Whether or not even corrected distances should be
turned into a tree that is supposed to be a "phylogeny" is also
debatable. But perhaps you, like me, just needed some way to
calculate % identity. Anyway, I will attach a current version of
my stack package. If you fail to get it, download a somewhat older
version @ ftp.bio.indiana.edu /molbio/mac/dnastacks_1xx.hqx where
xx is some version number (current is n7). Practice on DNA file
in the folder Sample Input & Output/Aligner Sample Data, to get
the named string format required. Go to a "utility card" in
DNA Translator stack and choose "String Nucleotides" from the Convert
menu. Somewhere in the resulting dialog there is a "Similarity
Matrix" (?) or similarly named choice.
Cheers,
Doug
--
Doug Eernisse <DEernisse at fullerton.edu>
Dept. Biological Sciences MH282
California State University
Fullerton, CA 92634
