sequence assembly software
little at ERE.UMontreal.CA
Thu Feb 18 13:09:38 EST 1993
veklerov at spindle.ee.lbl.gov (eugene veklerov) writes:
>I am trying to locate the existing software packages for sequence assembly.
>The package we are currently using is XDAP. There are 2 other similar
>packages made by private companies, but they are not available on the Sun.
>I also know that the Baylor College of Medicine is in the process of
>writing such a package.
>Does anyone know if there are other similar software packages available
>on the Sun?
One I evaluated was the assembly package from Millipore. It is part of
the Bioimage system. It performed very slowly- over 5 hours were required
to assemble a set of 170 sequences that were assembled in <10 minutes on
the xdap program of Staden. Steve Smith, who is now working on this, told
me some months ago that they were working on improving its performance.
They may have done so already. The real advantage of the Bioimage system
is that you can call up images of sequencing gels where there are ambiguities
in the sequence. The ambiguities can then be resolved by eye on the screen.
This requires that you use their image acquisition and sequencing software,
Other packages include:
1) GDE's assembly program (see Dan's posting). I find this rather
unfriendly and underpowered compared to xdap;
2) I heard that GCG was working on a Sun version which I imagine would
include their assembly component.
I hope this helps,
E-mail: little at ere.umontreal.ca Tim Littlejohn
Snail Mail: Departement de biochimie Phone: (514) 343-7936
Universite de Montreal Fax: (514) 343-2210
C.P. 6128, succursale A,
Montreal (Quebec), H3C 3J7
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