GeneMapper: Reference based annotation

GeneMapper is a program for transferring annotations from a well annotated reference genome (such as H. sapiens or D. melanogaster) to other (possibly unfinished) genomes. The rationale behind developing reference based systems such as GeneMapper is that although a lot of resources have been invested in annotating genomes of model organisms, it is unreasonable to expect similar efforts to be expended for the myriad of genomes that are now being sequenced. Lack of genome-wide full length cDNA sequences for these newly sequenced genomes makes it virtually impossible to completely annotate these genomes using cDNA based methods. GeneMapper provides an alternative method for obtaining high quality annotations of these genomes by transferring reference annotations. It is being used to annotate newly sequenced vertebrate, insect and worm genomes. The picture above shows the ortholog of a Drosophila melanogaster gene with two isoforms (blue), annotated in Drosophila pseudoobscura by GeneMapper (red).

We have compared GeneMapper with two other reference based annotation programs using a benchmark data set of orthologous human and mouse genes (Projector test set, Myer and Durbin 2004). The human annotations were used as reference to predict genes in mouse. The accuracy of the programs is summarized below (this table, as well as more details and other results appear in our paper). Note that Genewise is more suitable for aligning proteins to genomic sequence, and Projector may be highly accurate in cases where its underlying pairHMM suitably models the evolution of the genes.

GeneMapper is a C program developed by Sourav Chatterji working with Lior Pachter. The software can be downloaded here . The methods are explained in:

S. Chatterji and L. Pachter, Reference based annotation with GeneMapper, Genome Biology 7 (2006), R29.