AA alignments to DNA alignments!?

gonzalez at evalsb.geneti.uv.es gonzalez at evalsb.geneti.uv.es
Thu Jun 24 03:52:39 EST 1993


In article <930623123624.22800c13 at BOBCAT.CSC.WSU.EDU> THOMPSON at WSUVMS1.CSC.WSU.EDU ("Steve Thompson: VADMS genetics") writes:
>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
>

Following this thread, I want to add that at this Bioinformatics Service
we have developed a small program that will take the output from a
multiple alignment of peptides performed with CLUSTAL and the corresponding
nucleotide sequences, in a separate file, and then will write a file with
the multiple alignment of nucleotides corresponding to the one obtained
for peptides.
Although the program was written for our local users (i.e., it may be
a little sloppy for good programmers standards) I think it can be helpful.
The source code is Pascal and can be obtained upon request to the address
below.
 Hope this also helps.

Fernando Gonzalez
Dept. of Genetics and Bioinformatics Service
Univ. of Valencia, Spain
e-mail : gonzalez at evalsb.geneti.uv.es




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