DNA analysis programs

Greg Denomme denomme at FHS.CSU.MCMASTER.CA
Sat Mar 12 00:21:07 EST 1994

Dear Netters,

On 4 Mar 1994 Klaus.Matthaei at anu.edu.au wrote:

> I have been using MacVector for some years and am reasonably happy with it.
> HOWEVER I have recently added Assemblylign (meant to do alignments and
> compilations of contigs etc etc for ~$A1,000) to the package and it is very
> poor in its ability to align different sequences.  I can sometimes find 40
> bases of TOTAL homology between two sequences by eye and the program cannot
> do so.  I complained to Stratagene here in Australia about it last year
> (October?) and they went to the US distributor.  So far I haven't heard
> back from them.  So its not to good a program with poorer backup service.
> Cheers, Klaus
> --------------------------------------------------------------------------

To my knowledge Assemblylign is NOT meant to do "alignments" of DNA
sequences.  For example it was not designed to align two DNA sequences
from the immunoglobulin gene superfamily.  The purpose of Assemblylign is
to use it as a tool for the compilation of contigs - to compile
overlapping sequences with gaps to maintain homology.  We are using it to
keep track of data from exo-deletions of a 6 kb gene we are sequencing. 
The program gives use very good homology of "overlapping" sequence data
from one plasmid to the next.


No affiliation with Mac or the makers of Assemblylign

Gregory Denomme, PhD
McMaster University
Department of Pathology
denomme at fhs.csu.mcmaster.ca

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