Alignment Software

Sharon R.Minnerath minne002 at maroon.tc.umn.edu
Mon Sep 25 11:02:38 EST 2000

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


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