Determining heterologous sequences

Michael A. Lonetto lonetto at CGL.UCSF.EDU
Mon Dec 4 12:57:14 EST 1995

>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,

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:


It's an excellent alignment editor as well, and the only thing I miss
about VMS.


Michael A. Lonetto   lonetto at cgl.ucsf.edu
UCSF Dept. of Stomatology, 513 Parnassus Ave, San Francisco, CA 94143-0512
Check out my home page!     http://terminator.ucsf.edu/people/lonetto.html

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