AA alignments to DNA alignments!?

Steve Thompson: VADMS genetics THOMPSON at WSUVMS1.CSC.WSU.EDU
Wed Jun 23 14:36:24 EST 1993


Hi all -

In Message-Id: <9306231808.AA00773 at net.bio.net> ahouse at hydra.rose.brandeis.edu
(Jeremy John Ahouse) describes a problem that I have been complaining about for
years.  Since it makes so much more biological sense to align amino acids...

>    I have done a series of multiple alignments.  The alignments were done
>with inferred amino acid sequences.  Now that I am happy with the
>alignments I want to go back to the mRNA sequence (which I have) for some
>of the clustering and parsimony analysis.  I want to enforce the alignments
>(gaps, etc...) from the aa's on the nucleotide alignment.
>
>    I know I can do this by hand, but are there any tools that help with
>this, that you all know about?

To date I am aware of two programs which can automate this problem:

1) Doug Eernisse's (Doug_Ee at um.cc.umich.edu) Mac-based HyperCard Stacks "DNA
   Translator and Aligner" have this capability.

2) Joe Felsenstein's PHYLIP package (ftp to evolution.genetics.washington.edu)
   now (version 3.5) has an unsupported program named MakeInF which supposedly
   also can perform the dirty deed.

I have NOT used either of these programs, so I can not attest to how well they
work.  Another point to consider is the new PHYLIP as well as still having
ProtPars for protein parsimony analysis now has the program ProtDist to allow
the use of Distance method algorithms with protein data.  I HAVE used this
approach and it works great!

						Hope this helps, Steve 

                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                  BITnet:  THOMPSON at WSUVMS1 or STEVET at WSUVM1
                   INTERnet:  THOMPSON at wsuvms1.csc.wsu.edu





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