assmebly software

Deverie K. Bongard-Pierce bongard at FRODO.MGH.HARVARD.EDU
Thu Dec 9 11:43:51 EST 1999


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.

-----------------------------------------------------
Deverie K. Bongard-Pierce
Sr.Tech./Lab Manager- Howard Goodman's Lab
Dept. of Molecular Biology       Fax: (617) 726-6893
Mass. General Hospital            Lab: (617) 726-5938
Boston MA 02114
email: bongard at molbio.mgh.harvard.edu
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