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