I have recently started using GCG to do some alignments.
I have 35 or so sequences,of a kb or so in length, and I have had no problem
using pileup to align them in a fairly believable fashion.
But I am having problems getting software to output a consensus sequence,
lineup will only allow 30 sequences, and consensus seems to have a maximum
length of 150 bp.
I am sure I just need to read the documentation more thoroughly but I would
be grateful for any assistance.
If anyone knows of a resource with examples of e.g. how to create a pileup,
how to search for interesting motifs etc I would also be very grateful.
I WILL go on a course, but I would like results now!