The code here is/was used to generate and display information on protein-coding
genes within T1DBase, which is a website for the
type 1 diabetes research community. I developed the Gene Models code
while working on T1DBase,
between Jan. 2006 and Dec. 2008. The code is described in detail in
a blog post, which you might find easier to read in
PDF format 
.
.
There are two elements to the Gene Models code:
- A set of Perl scripts that download gene/transcript data from various websites,
convert it to GFF format, store it in a database, and eliminate
or highlight conflicting information. Everything is controlled by
one script,
generate_gene_models.pl. - A set of Perl modules that display the gene model data, and calculate summary views. (These modules aren't stand-alone, and work within the framework of the T1DBase website - but they shouldn't be hard to modify, so email me (see footer) if you're interested in using this code.)
If you want to look at the code without faffing around with compressed files:
-
GeneModel
- scripts
- Specification
- Collection.pm
- Specification.pm
- Utilities.pm