help with consensus sequence

Keith Elliston elliston at msdrl.com
Tue Aug 11 12:54:17 EST 1992

lamoran at gpu.utcs.utoronto.ca (L.A. Moran) writes:

: 3. align amino acid residues manually using a word processor
: 4. convert to nucleotide alignment by codons
: 5. derive a consensus manually taking into account the phylogenetic
:    distance between species and ignoring biases such as a large number
:    of genes from closely related organisms
: In my opinion it is wrong to assume that any computer program can do a
: better job than an intelligent human when it comes to multiple sequence
: alignments and deriving a consensus.

I can't let this one go by without a comment...

When you are dealing with very conserved sequences, the human eye (brain) can 
align sequences pretty well, but when dealing with more distant relationships,
the computer is a really big help.  

Thus, I would suggest using a multiple alignment program on some system (I
don't know of one that runs on the mac and is PD/shareware), and then OPTIMIZE
the alignment manually.  I will agree that most (the ones I have used)
multiple alignment programs don't align sequences exactly the way I would
like, but it is usually fairly easy to edit what they give you to end up with
a very good alignment.

Also... doesn't PIMA work with coding sequences when aligning proteins, or
something like that?  Anyone know?

Also*2...  for doing phylogenetic analyses on the MAc, PAUP, written by David
Swofford and available for about $50, is a great program.


Keith O. Elliston            elliston at msdrl.com           uunet!av8tr!elliston
AA5A/U  N9734U             elliston at mbcl.rutgers.edu     elliston at biovax.bitnet
"Beware of pseudo-experts with a mission and a grudge, especially if they are
 lawyers pretending to be scientists." -- H.W. Lewis in 'Technological Risk'

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