IUBio

sequence alignment

Aidan Weatherill Aweather at worf.molbiol.ox.ac.uk
Tue Oct 27 05:58:13 EST 1998


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!

yours grovelingly

Aidan.





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