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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.

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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