Source Code for:

Quantitative Measures for the Management and Comparison of Annotated Genomes

Karen Eilbeck, Barry Moore, Carson Holt and Mark Yandell

PDF:

PDF of the BMC Bioinformatics Paper

Overview:

The software available on this page were used to measure the complexity of gene annotations and the distance between two transcript annotations as described in the paper above.

Software:

The code used in this paper is available for checkout from our Subversion repository. You will be checking out the latest unreleased revision of the Comparative Genomics Library (CGL) which will include four scripts named splice_complexity_exonic, splice_complexity_nucleo, splice_distance_exonic and splice_distance_nucleo. Each file has a usage statement that explains their use. CGL has some dependencies and you can get guidance for installing these dependencies by visiting the CGL Installation page on our web site. However, note that you will be following those instructions to install dependencies only, and then getting the CGL code and scripts used in this analysis by checking out the latest revision of CGL from svn as described below.

To check out the CGL code:

svn co svn://topaz.genetics.utah.edu/CGL/trunk/ CGL