DNA analysis programs

[Klaus.Matthaei at ANU.EDU.AU]

>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. 
^^^^^^^^^^^^^^^^^^^^
Exactly my point it is supposed to compile overlapping sequences and
assemble them as a contig and it couldn't for me, even when there was a
60bp TOTAL homology overlap.  I would be interested to hear if I am
misusing the program (I doubt that since I have been a Mac user since its
inception) or is there a bug in my version of the program.  Either way I
still haven't heard back from the supplier.
Cheers, Klaus

 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.
>
>Cheers,
>Greg
>
>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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Klaus Matthaei
Gene Targeting
The John Curtin School of Medical Research
The Australian National University
PO Box 334, Canberra, ACT 2600, Australia
E-mail: Klaus.Matthaei at anu.edu.au

"Think twice - Do once"
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