[BiO BB] Re: EST clustering
Rick Westerman
westerman at purdue.edu
Mon Dec 15 17:15:37 EST 2003
Chris Dwan asks:
>I am very interested to hear about how other shops do their EST analysis
>these days.
For the following two steps we use the 'stackpack' program from Electric
Genetics
>2) Assemble contigs
> - We use phrap, mostly because we have some expertise with it.
> There are other options available. My opinion is that it's better
> to use a tool that is well understood at your lab than to try to
> learn an unknown that may or may not be better.
>
>3) (optional) go through the contigs and break up those that do
> not have good support across their entire length. This is currently
> a real pain, but hopefully we'll have an automated system trained
> "real soon now."
Annotation and other post-EST assembly steps are project dependent. Blast
and HAMMER certainly play a role here.
-- Rick
Rick Westerman
westerman at purdue.edu
Phone: (765) 494-0505 FAX: (765) 496-7255
Department of Horticulture and Landscape Architecture
625 Agriculture Mall Drive
West Lafayette, IN 47907-2010
Physically located in room S049, WSLR building
Bioinformatics specialist at the Genomics Facility.
href="http://www.genomics.purdue.edu/~westerm"
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