Pretty is the program for consensus of aligned sequences.
In SeqLab, the editor will also compute a consensus sequence.
Several special effects can be had by weighting the consensus
or other sequences; you may need to run pretty twice once using
the -ugly switch to achieve the final result.
Nick Staffa, CMB telephone 361-5444 ext 410
Scientific Computing Support Group
ITSS contractor
National Institute of Environmental Health Sciences
Research Triangle Park, North Carolina
Debra Parrish, DIR monitor.
> ----------
> From: Aidan Weatherill
> Sent: Tuesday, October 27, 1998 5:58 AM
> To: info-gcg at net.bio.net> Subject: sequence alignment
>> 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.
>>>
