title: GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads.
abstract: BACKGROUND
  The reliable identification of genes is a major challenge in genome research, as further analysis depends on the correctness of this initial step. With high-throughput RNA-Seq data reflecting currently expressed genes, a particularly meaningful source of information has become commonly available for gene finding. However, practical application in automated gene identification is still not the standard case. A particular challenge in including RNA-Seq data is the difficult handling of ambiguously mapped reads.
  
  
  RESULTS
  We present GIIRA (Gene Identification Incorporating RNA-Seq data and Ambiguous reads), a novel prokaryotic and eukaryotic gene finder that is exclusively based on a RNA-Seq mapping and inherently includes ambiguously mapped reads. GIIRA extracts candidate regions supported by a sufficient number of mappings and reassigns ambiguous reads to their most likely origin using a maximum-flow approach. This avoids the exclusion of genes that are predominantly supported by ambiguous mappings. Evaluation on simulated and real data and comparison with existing methods incorporating RNA-Seq information highlight the accuracy of GIIRA in identifying the expressed genes.
  
  
  METHODS
  GIIRA is implemented in Java and is available from https://sourceforge.net/projects/giira/.
authors.affiliation: Research Group Bioinformatics (NG4), Robert Koch-Institute, Nordufer 20, 13353 Berlin, Germany.
authors.forename: Franziska
authors.initials: F
authors.lastname: Zickmann
authors.forename: Martin S
authors.initials: MS
authors.lastname: Lindner
authors.forename: Bernhard Y
authors.initials: BY
authors.lastname: Renard
mesh_terms: D000465:Algorithms; D000818:Animals; D004926:Escherichia coli / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D005796:Genes; D023281:Genomics; D006801:Humans; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*