Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

Background: In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. However, such evidence is often incomplete and usually uncertain. The extrinsic evidence is usually not sufficient to recover the complete gene structure of all genes completely and the available evidence is often unreliable. Therefore extrinsic evidence is most valuable when it is balanced with sequence-intrinsic evidence. Results: We present a fairly general method for integration of external information. Our method is based on the evaluation of hints to potentially protein-coding regions by means of a Generalized Hidden Markov Model (GHMM) that takes both intrinsic and extrinsic information into account. We used this method to extend the ab initio gene prediction program AUGUSTUS to a versatile tool that we call AUGUSTUS+. In this study, we focus on hints derived from matches ...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern, Stephan Waack
• Keywords: BMCBI 2006, Extrinsic Evidence, Gene Prediction, Gene Structure