In article <60olra$2cj at gap.cco.caltech.edu>,
mathog at seqaxp.bio.caltech.edu writes:
[...]
> Anyway, in summary, if you must attack this problem, use a good sequence
> assembly program (gelassemble in GCG can handle a fair amount of this EST
> noise), edit each pile of ESTs down to a single consensus sequence, and then
> align the consensus sequences.
[...]
Whatever EST project maintainer are claiming(1), it is the better
way to analyse ESTs which ARE part of a "sequencing project" due to
the presence of partial cDNA. And, also, this is the only way to
go through annotations/orientation/garbage regions problems without
to much efforts.
Just a note, gelassemble is based on the Staden method, so
that if you don't have access to the GCG package, you can try the
Staden one.
François.
(1) This is not for you, Sean, before beginning any EST project, we
should have make standard specifications. But, this is an old and
redundant debate.
--
François Jeanmougin | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
