[Bioperl-l] SimpleAlign/AlignIO

[Chris Fields]

Bernd,

I'm not sure it's a good idea to constrain the entire alignment (and  
all sequences contained within) to a single alphabet.  For instance,  
what if I wanted to align a translated (protein) sequence, possibly as  
3- or 6-frame, to a DNA sequence of interest?  Or if I wanted to align  
a Meta sequence w/o an alphabet (i.e. a structural consensus sequence)  
with a DNA/RNA/protein sequence?  The former example is fairly common  
and may not be entirely possible with SimpleAlign (I haven't tried it  
to tell the truth), but the latter is what I do with the Stockholm  
parser.

chris

On Sep 18, 2008, at 12:34 PM, Bernd Web wrote:

> Hi,
>
> Possibly I overlooked this, but is it not possible to supply an
> alphabet to SimpleAlign?
> When SimpleAlign starts making sequence objects _guess_alphabet is
> executed and in case the sequence (slice) only contains gaps a warning
> is raised as the alphabet cannot be guessed.
> As all sequences in the alignment (generally) would be of the same
> type, it could be good to set the alpabet for the alignment; this also
> would prevent the executing of _guess_alphabet for all sequences. Is
> this possible?
>
>
> Regards,
> Bernd
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign