Hi, I am tryning 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
Conventiopnal 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
