Gene Finding

With advancements in high throughput sequencing technologies, complete genomic sequences of novel species are becoming more and more abundant. Given a new genome, one of the most important tasks is determining the structure of its protein-coding genes. This procedure is known as gene prediction or gene finding, which is essential for genome characterization and allows downstream bioinformatics applications, such as functional annotation.

This functionality can be found under Genome Analysis → Gene Finding, a submenu with two entries, Eukaryotic Gene Finding and Prokaryotic Gene Finding. Each entry opens a wizard whose first page lists the tools available for that type of organism.

Two gene finding strategies are available:

• Eukaryotic Gene Finding: Two tools are available for eukaryotic genomes. AUGUSTUS predicts genes ab initio from a model trained for a particular species, and is one of the most accurate programs for the species it is trained for. EviAnn instead builds gene models from evidence, combining RNA-seq or transcript alignments with protein homology from related species, which needs no species-specific training and no repeat masking.
• Prokaryotic Gene Finding: The Prokaryotic Gene Finding functionality is based on Glimmer, which is a system for finding genes in microbial genomes (bacteria, archaea, and viruses). Glimmer uses Interpolated Markov Models (IMMs) to identify the coding regions and to distinguish them from noncoding DNA.