PC sequence alignment program

Stuart Brown browns02 at mcrcr.med.nyu.edu
Wed Feb 24 13:13:11 EST 1999


In article <4.1.19990223150822.0093bb30 at genetics.uiowa.edu>,
tremby at GENETICS.UIOWA.EDU (Yuri Trembath) wrote:

> Dear all,
> 
> Sorry to raise a mildly ancient topic for some of these newsgroups, but I'd
> be interested in hearing opinions on any and all sequence alignment
> programs for Windows95/98/NT PCs.  I'm looking for something that will read
> ABI sequence files and allow me to do multiple alignments and export
> consensus sequences for BLAST searches.  Identification of restriction
> sites, exons, repeats, ORFs, etc. would be bonus.  Cost comparisons would
> also be appreciated.
> 
> Thanks in advance,
> 
> Yuri Trembath
> University of Iowa

Sequencher from Gene Codes Inc. now has a Windows version.  
It is about $2000.
<http://www.genecodes.com/>

This is by far the best and easiest to use program for analyzing
ABI sequence files to create contigs/consensus sequences.  
Its best feature is alignment of the chromatograms so that you
can easily spot the cleanest read for conflicts between overlapping
sequences. It does a very nice job on restriction mapping,
but not so good on ORFs (just looks for ATG and Stop codons)

-- 
Stuart M. Brown
Bioinformatics Consultant
NYU Medical Center, 550 First Ave, NY, NY




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