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.
Jean-Manuel
