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Alignment of coding sequences

Doug.Eernisse at UM.CC.UMICH.EDU Doug.Eernisse at UM.CC.UMICH.EDU
Sat Mar 20 16:36:36 EST 1993

> From: gartmann at VMS.MPIIB-FREIBURG.MPG.dbp.de > Sender:
list-admin at daresbury.ac.uk > 
> Hello, 
> just a simple question: is there a program that can display multiple 
> sequence aligments using different colors for different sequence 
> characters? It should run on VMS (REGIS) or MacIntosh.
My HyperCard stack, Aligner, does sequence coloring that you
might find useful. If you just want AGCTU to be different colors,
you are probably better off with one of the other available
editors. I only recommend using the coloring if you want to do
some of the coloring routines unique to Aligner, for example, for
doing screen captures in order to make seminar slides or
whatever. Example routines that are different than other editors
1) color valid amino acid 1-letter symbols. 
2) color amino acid 1-letter symbols according to their properties 
   such as hydrophobicity, chemical properties, etc. 
3) color every triplet of nucleotides according to amino acid coding
   or amino acid properties as in #2.
>> From: jasons at bmc.uu.se 
>> Does anyone know of a program that will limit the addition of gaps 
>> in an alignment to mulitples of three when the sequences being compared 
>> are known to be coding sequences? >> 
> From: GGUTMAN at vmsc.oac.uci.edu 
> A better solution might be to align the amino acid sequences, then
> replace them with their corresponding nucleotide sequence. 
> George 
Aligner also has a facility to align corresponding nucleotide
sequences based on your amino acid alignment. Your DNA/RNA and AA
alignments must start at the same place and be in the same order.
If so, you can align the amino acids, the select "Create Nuc
Gaps" from the menu, select the DNA/RNA alignment from the open
dialog, and during import to another Aligner card of your
choosing, Aligner will strip any gaps present, then put triplets
of gaps in places corresponding to your amino acid alignment. I
find this is very useful for primer design, for example,
especially when coupled with #3 on coloring above.
I am rewriting this as a C application so eventually all this
might get faster and smaller with an improved interface 8^}
Version 1.0M3 of Aligner and another stack, DNA Translator, are
available for anonymous ftp at 'um.cc.umich.edu', directory
'gdef', file name is 'DNAstack.hqx' which will get the entire
package in binhexed format. HyperCard 2.1 with the RAM partition
set to 3 (or better 5) MB is recommended because of the large
card size and coloring routines.
Doug Eernisse

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