tools and options for EST consensus sequences

Sylvain Foisy sylvain.foisy at bioneq.qc.ca
Mon Nov 3 07:06:01 EST 2003


Hi,

In article <egznflvcyd.fsf at sefirot.ii.uib.no>, ketil+news at ii.uib.no 
wrote:

> I'm looking for tips on how to tune current tools for EST consensus
> sequence generation.  I'm currently trying out Phrap, CAP3 and the
> TIGR assembler, and just running them on the sequences (from UniGene,
> no chromatograms or quality information) without specifying any
> particular options.  I'm curious what experiences people have with
> assembling ESTs, and what options they you find optimal.

We have tried StackPack from Electric Genetics and found it pretty good 
although the group working with us decided to create their own EST 
clustering pipeline.

E-mail me if you want more details.

> Thanks for any guidance,

No problem

Sylvain

Sylvain Foisy, Ph. D.
Project Manager
BioneQ - Reseau quebecois de bio-informatique
Genome Quebec / Universite de Montreal
Montreal,Quebec
Canada
sylvain.foisy at bioneq.qc.ca





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