[BiO BB] Re: EST clustering

[Rick Westerman]

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"