Alignment Software

Scottie Adams sadams at northnet.org
Wed Sep 27 09:45:41 EST 2000

Hi Sharon

	I have used Sequencher for the past  5 or 6 years and find it to be
the fastest, easiest to use alignment software.  It can't be beat for speed
and simplicity.  I believe if you go the webpage for GeneCodes
http://www.genecodes.com/, you can  download a  demo copy for a Mac or send
away for a PC version.  The Mac version is considerably cheaper than the PC
version.  I have worked with the people at Genecodes extensively and their
tech support is great ( although it is so intuitive, you rarely need them).

I would at least check out Sequencher before making any decisions.


>Hello Everyone,
>I have a question about Alignment Software.  I am currently sequencing a
>BAC which I am told is about 340 kb.  I have it nebulized and subcloned
>into Bluescript.  I sequence on a LI COR 4200 and get 700-1100 bp per
>sample.  I have been using the LI COR AlignIR program  to assemble and
>have crashed the program.  I was told to put the contigs into a new
>project to save space, but at this point (85 kb) I have a few 5 kb
>contigs, but most samples haven't matched up yet, so this isn't
>feasible.  I have access to the McVector/AssemblyLIGN program (Mac
>version), but the company isn't able to tell me how many samples this
>program can work with or whether a project of this size is feasible.
>Is it feasible to assemble a project this large on a personal computer?
>Do you think the McVector/AssemblyLIGN program would work?  Do you think
>some of the other assembly packages out there would work (such as
>Sequencher?) If so, who is the vendor and what is the cost?
>Do I need to go to a Unix Platform?  I would have access to a UNIX
>system (Phap/Phred) for about $500.00 per year.
>Any comments or suggestions would be greatly appreciated.  Thank you in
>Sharon Minnerath

Scottie Adams aka Pamela Scott Adams
ABRF Fragment Analysis Research Group

Molecular Biology Core Facility
Trudeau Institute
100 Algonquin
Saranac Lake, NY    12983
Phone:  518-891-3080
Fax:    518-891-5126
Email: sadams at northnet.org


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