EST clustering and assembling

Simon Andrews simon.andrews at bbsrc.ac.uk
Mon Jan 28 05:10:28 EST 2002


Andrea Hansen wrote:
> 
> Hi,
> 
> is there anybody with experience in clustering and assembling of
> EST data? 

We use the Staden package for our assemblies.  It generally does a
reasonable job of assembly (usually resulting in separate contigs for
splice variants).  You need to play around a bit with the assembly
parameters to get as much together initially as possible.

We have assembled groups of >100 related ESTS very quickly.  We tend to
just use a blast search of an EST database to generate potential members
of the set.  Staden will itself reject anything which doesn't appear
similar enough to fit into the assembly.

Hope this helps

Simon.




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