Alignment Software

James VanEe jiv2 at cornell.edu
Tue Sep 26 08:46:59 EST 2000

LaserGene's SeqManII claims a 64,000 read capacity: 

I can't say for sure, but I think Sequencher would handle it.

I'm not very familiar with macVector/AseemblyLIGN.

$500/year isn't much if you can handle whatever learning curve you'll 
have with unix.  An alternative is to purchase or recycle inexpensive 
hardware and use linux (free). Similar learning curve and technology 
hassles to consider.

What about the Staden package?

Now a relevant question:  How is Phred/Phrap actually going to do on 
LiCor Data?  the assembly depends on the phred quality calls and I 
would like (well, need) to know how reasonable those calls are for 
li-cor data.

>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

James VanEe                              Phone: (607) 254-4862
BioResource Center
Computing Facilty
170/171 Biotech Bldg                       Fax: (607) 254-4847
Cornell University
Ithaca, NY 14853                 www: http://brcweb.bio.cornell.edu


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