[BiO BB] Gene prediction
Yannick Wurm
idh at poulet.org
Thu Dec 7 08:24:09 EST 2006
Hi,
we all know that gene predictions can be far from reliable. Which is
why recent genome projects, such as the Honey bee, used several gene
predictions: ab initio predictions, homology-based predictions, EST-
based prediction... They used GLEAN3 to combine the different
predictions into one confident "Official Gene Set".
I am exploring my favorite - currently unannotated - genome. Does
anyone know of a web-tool which might do something similar on a much
smaller scale? (I basically just want the CDS sequences for a small
number of genes). If not, this could be a great opportunity for
someone....
Input:
my small genomic sequence of interest (maybe 10 or 20kb) + ESTs +
other homologous sequences I may have
Program fetches more homologous sequences from Genbank.
Aligns everything it can to my sequence of interest
Program uses genscan or whatever to predict exons.
Program figures out a "consensus" protein sequence and determins
introns/exons.
Any ideas? Comments?
Cheers,
yannick
--------------------------------------------
yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
http://www.unil.ch/dee/page28685_fr.html
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