sequence assembly

Mike Gruidl mgruidl at com1.med.usf.edu
Sat Jun 8 15:49:45 EST 1996


Bernard Murray wrote:
> 
> 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
> >DNASTAR.
> >
> >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
> 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)


I have a copy of a program called 'cap' for contig assembly program.  
The program was originally written for Unix, but was compiled to run in 
dos.  I've used it and it works very well and very quickly.  I believe 
this is the same program that is used in Don Gilbert's Seqpup.  I did 
not compile the program and I am not the original author.  but I will be 
happy to share what I know.

Mike




More information about the Bio-soft mailing list