title: Using intron position conservation for homology-based gene prediction.
abstract: Annotation of protein-coding genes is very important in bioinformatics and biology and has a decisive influence on many downstream analyses. Homology-based gene prediction programs allow for transferring knowledge about protein-coding genes from an annotated organism to an organism of interest.Here, we present a homology-based gene prediction program called GeMoMa. GeMoMa utilizes the conservation of intron positions within genes to predict related genes in other organisms. We assess the performance of GeMoMa and compare it with state-of-the-art competitors on plant and animal genomes using an extended best reciprocal hit approach. We find that GeMoMa often makes more precise predictions than its competitors yielding a substantially increased number of correct transcripts. Subsequently, we exemplarily validate GeMoMa predictions using Sanger sequencing. Finally, we use RNA-seq data to compare the predictions of homology-based gene prediction programs, and find again that GeMoMa performs well.Hence, we conclude that exploiting intron position conservation improves homology-based gene prediction, and we make GeMoMa freely available as command-line tool and Galaxy integration.
authors.affiliation: Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, D-06484 Quedlinburg, Germany jens.keilwagen@jki.bund.de.
authors.forename: Jens
authors.initials: J
authors.lastname: Keilwagen
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Wenk
authors.affiliation: Schattat Lab, Institute of Biology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Erickson
authors.affiliation: Schattat Lab, Institute of Biology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany.
authors.forename: Martin H
authors.initials: MH
authors.lastname: Schattat
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Grau
authors.affiliation: Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, D-06484 Quedlinburg, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Hartung
mesh_terms: D000465:Algorithms; D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D029441:Carica / Q000235:genetics; D002645:Chickens / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007438:Introns / Q000235:genetics; D051379:Mice; D008957:Models, Genetic; D058977:Molecular Sequence Annotation / Q000379:methods*; D012275:Oryza / Q000235:genetics; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D011198:Solanum tuberosum / Q000235:genetics; D014026:Nicotiana / Q000235:genetics
chemical_list: D012333:RNA, Messenger