sequence assembly

Bernard Murray bernard at elsie.nci.nih.gov
Fri Jun 7 18:49:15 EST 1996

In article <31B68CAC.710C at imb-jena.de>, dbauer at imb-jena.de says...
>I know 2 program packages for IBM:
>PC/GENE runs under DOS and
>DNASTAR, both for DOS and Windows.
>They have also modules for contig assembly. I used both and prefer
>ALEX NECHIPORUK/CSMC/TEL 310 855 7612 wrote:
>> I am sequencing a novel gene.  We pulled multiple cDNAs from the libraries.
>> After they fully sequenced I'll have to align all sequences together.
>> Can anyone recommend a user friendly software (I prefer PC-DOS or
>> Windows based) for multiple sequence fragment assembly.

It may be worth a glance at a publication by a colleague of mine;

Miller, MJ & Powell, JI (1994)
"A quantitative comparison of DNA sequence assembly programs"
J. Computational Biol. 1, 257-269

It turns out that some commercial offerings are extremely poor
at performing assemblies - even when the fragments have a very
low proportion of errors.  If you want more details you can
get hold of Dr. Miller as mark at elsie.nci.nih.gov
I believe that the then version of PC/GENE was particularly
bad but that the company has since improved the program
considerably.  I don't think Mark tested DNASTAR.

Bernard Murray, Ph.D.
bernard at elsie.nci.nih.gov  (National Cancer Institute, NIH, Bethesda MD, USA)
"He's like an idiot savant -- minus the savant." -Crow T. Robot, MST3k
                                (The Skydivers)

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