sequence assembly software

Littlejohn Tim 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,
however.
 
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,


Tim


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