How To Extract Introns Positions And Domains From Entrez Gene Xml?

Question

[Dror]

Entrez gene XML is very complicated, is there a way to extract all the genomic information (exon-introns positions) and the assigned protein domains positions in an automatic way from the XML ?

In other words: where in the Entrez GENE XML I could find the introns annotation and can I found the domains annotations?

If anyone has a python or perl scripts that can do that please share.

Answer 1

[Joachim]

Hi!

There is a paper out about a Perl implementation that can efficiently process Entrez Gene XML: http://bioinformatics.oxfordjournals.org/content/21/14/3189.full

Their software is still available at http://sourceforge.net/projects/egparser/, but it has not been updated for a couple of years now.

Joachim