sequence alignment

Staffa.Nick staffa at NIEHS.NIH.GOV
Tue Oct 27 09:22:30 EST 1998

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.

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