Gene prediction and an EST

Simon Andrews simon.andrews at
Thu Feb 20 03:37:59 EST 2003

bob wrote:
> It maps to a genescan gene, that predicted gene is not complete.  it
> gave me one more exon, but I still need more.  That is why I asked if
> extending a known EST was possible.
> cAn genewise predict a gene with a starting EST ?

If you know the genomic position in Ensembl then you can see the
positions of any surrounding ESTs by looking at the EST and EST
transcript tracks in the genome browser (turn them on from the Features
menu in the genome browser if you can't see them).  A genscan prediction
on its own without EST coverage to back it up is a rather flimsy start
for an investigation.  You still didn't say what organism you're working
with, but for both human and mouse there must be very few genes (or gene
forms) that haven't turned up a few times somewhere in an EST collection

> > If you're still getting nothing you can BLAST search the ESTs to find
> > overlapping sequences then use a sequence assembly package (Staden,
> > Sequencher etc) to assemble them into a longer contig - but hopefully
> > that's all more hassle than you need!
> >
> Tried that.  No luck.  I'm either unlucky or doing something wrong.
> Perhaps I should forget this in-silico stuff for now and just do a 5'
> RACE.  Doing it manually in the age of the genome project.  How retro
> ;-)

If you really can't find any other evidence to support your EST then its
back to the bench for you!  Look on the bright side though, if this is a
completely novel gene then it means a more interesting paper (patent?)
at the end of it.


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