Trace Editors for Macs

Paul Morrison morrison at FARBER.HARVARD.EDU
Fri Oct 29 17:42:41 EST 1993


Harry Mangalam, VCO/Micro+Mol Genetics, Irvine Hall, Coll of Med, UC
replied to kinneya at esvax.dnet.dupont.com:

>In article <9310251805.AA10757 at esds01.es.dupont.com>,
>kinneya at esvax.dnet.dupont.com wrote:
>> 
>> >I'm looking for Macintosh-based software to help us edit ABI-format
>> >sequence files.  I would like something like the unix-based TED, which
>> >prints the ABI-called sequence beneath the DNA migration absorption
>> >curves and allows you to make adjustments.
>> 
>> The "EDITSEQ" sequence editor software for the Mac from DNAStar (which is
>> also part of their Lasergene package) will do this.
>> 
>> Their phone number is (608)258-7420
>
>   So will Sequencher, from Gene Codes (and is very expensive if all you're
>looking for is an editor), but is a complete, powerful, and very easy to
>use fragment assembly program.  Their phone number is: 313 769 7249; ~$1200
>w/ hardware lock, site/multiple copy discounts. 
>   IMHO, Sequencher is the much better of the two for editing and fragment
>assembly, but it is not a 'full-featured' Sequence analysis pkg ie no
>protein analysis, not a lot of DNA analysis, which Lasergene does offer.
>
>
>Std Disclaimers..
>Harry
>

Yes indeed there is more than one contig builder out there and I agree
completely with Harry that Sequencher is the most powerful. One thing that
caught my attention in the original post was the wording "allows you to
make adjustments". Now if that is meant to mean make adjustments to the
called sequence by comparing to other sequences then yes, the programs
mentioned do this. If it means make adjustments to the raw data data signal
that comes out of a 373A so that one might be able to tweak paramaters so
that more sequence is called, I don't think that program exists. It becomes
evident after using the 373 for awhile that a program that would either
circumvent or enhance the algorithm in ABI's analysis program might be a
useful tool. What do I want this tool to do? 1) Allow me to get inside and
change the base space number if I want. 2) Figure a way to get around the
"all DNA is 25%A25%G25%C25%T" problem. These are _easy_ fixes. Others are
hard. I hear rumours and papers of neural net analysis of this data.
Anybody out there working on something that looks good? 

Paul Morrison   Dana1030
Molecular Biology Core Facility
Dana Farber Cancer Institute
44 Binney Street
Boston, MA 02115






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