Gene Models

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 pdf.
There are two elements to the Gene Models code:
  1. 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,
  2. 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.)
The code is available as either a gzipped tar file, or a 7-zipped file. Please note that the gene model scripts are being actively maintained by the current T1DBase staff, and that the code uses elements of BioPerl.