[Bioperl-l] ESTScan

Hilmar Lapp hlapp@gmx.net
Tue, 15 Aug 2000 12:46:53 +0200

As already mentioned earlier, we will very soon need an ESTscan parser
that translates the results into SeqFeatures. In general, this would
probably fit nicely in the GeneStructure (no more flames please, we will
bash this out) framework, as in the prediction made one or more predicted
CDS (predicted exon) is flanked by UTR regions.

The thing which is not covered are the insertions and deletions ESTscan
predicts, which cannot be cleanly represented in any of the SeqFeature
objects. One quick hack could be to annotate the indels as SeqFeatures,
too, but I'm not so happy with this. Maybe one could use something of the
Variation framework, but I have no overview on this, and after reading
the docs of DNAMutation and SeqDiff I'm getting the impression that it
wouldn't really be straightforward. Maybe Heikki or someone else who
knows better than I can comment on this.

If anyone has a good idea, I'd be glad to hear about it.

Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
A-1235 Vienna                                fax: +43 1 86634 727