assmebly software

Doug Eernisse DEernisse at fullerton.edu
Fri Dec 10 15:27:14 EST 1999


In article <l03130300b47583fa4af0@[132.183.189.39]>,
bongard at FRODO.MGH.HARVARD.EDU ("Deverie K. Bongard-Pierce") wrote:

> On 12/2 Pat Fan wrote
> >Does anyone know the capacity of some of the popular desktop sequence
> >assembly software?  ....
> 
> I routinely use Squencher3.1 on my MAC to assemble EST projects containing
> 10,000 sequences.  These sequences range in size from 100bp to 700bp- the
> average being around 400.  I have heard a rumor that Sequencher 4 can
> assemble projects larger then 10K sequences.  I believe that the version 4
> software is currently available for the PC but the MAC version is not quite
> out.
> 
> I too have used Phred/Phrap/Consed trio and while it is great for large
> assembly projects (>10K sequences) I find editing in Consed to be a bit
> clumsy & slow when compared with Sequencher.  It also does not output the
> data in a fashion thats easy to use with other systems & programs.
> Squencher does take longer to import the chromatographs and assemble the
> alignments then P/P/C but if you start a large project just before going
> home its usually done in the morning.  I find the time I save in editing
> with Sequencher to be will worth the longer setup times.
> 
> Version 3 of Sequencher does not do as well as the Phred/Phrap/Consed trio
> when it comes to aligning EST sequences with their genomic counterparts-
> alot more editing is need around intron borders,  but again I have heard
> that the ver.4 software does a much better job with these kinds of
> alignments.
> 


I just got a demo cd from the GeneCodes (Sequencher) folks and it
does suggest that their version 4 (so far only for pc but, given their
past preference of Macs, am sure that will change soon) has some
major enhancements. These include:

-- a "large gap" alignment algorithm to align cDNAs to genomic strand
-- improved partly automated editing of contig discrepancies
-- new options for editing sequences (replace, overstrike, or insert)
-- support for other sequencer formats besides ABI, incl. ALF, ALX,
   LI-COR and Beckman

Hope this helps.


Doug

-- 
Doug Eernisse
Department of Biological Science
California State University
Fullerton, CA 92834-6850 USA
<http://biology.fullerton.edu/deernisse/>





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