Determining heterologous sequences

Jean-Manuel Henry jjhenry at UCDAVIS.EDU
Wed Dec 6 16:39:06 EST 1995

On Mon, 4 Dec 1995, Michael A. Lonetto wrote:

> >Hi, I am trying to determine heterologous nucleotides in a set of
> >related sequences.  So far, I have been able to determine homologous
> >nucleotides, by performing a multiple sequence alignment and shading
> >homologouse regions,2 this isn't of much use since the remaining
> >sequences may hav homology with one another. For example:
> >sequence 1: A
> >sequence 2: A
> >sequence 3: A
> >sequence 4: C
> >sequence 5: C
> >sequence 6: T
> >Conventional shading programs would shade all sequences containing "A"
> >(1,2, & 3). However, I would like a program which would shade "C" as well
> >in sequences 4 & 5. That is, a program to detect all nonunique
> >nucleotides (T in sequence 6, in the above example). If anyone knows of a
> >program with this ability please email me. Much obliged,
> >JMH
> The only program I am aware of that does this properly is MALIGNED, by
> Stephen Clark.  Unfortunately it is VMS only as far as I know.  There
> is a version in the IUBIO archives:
> (ftp://iubio.indiana.edu/molbio/vax/maligned_v1_65b.uue)
> It's an excellent alignment editor as well, and the only thing I miss
> about VMS.
> Mike
Hi again, 
    I don't know anyhting about compiling and running programs on vms, 
but I am willing to figure it out... I just want to make sure that 
Maligned will detect non-unique bases in a multiple alignment. Can it ? 
Thanks again. 

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