title: SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.
abstract: BACKGROUND
  Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them.
  
  
  RESULTS
  SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data.
  
  
  CONCLUSIONS
  SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/.
authors: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St, W, Montreal, QC H4B 1R6, Canada. ian.reid@concordia.ca.
authors: Ian
authors: I
authors: Reid
authors: Nicholas
authors: N
authors: O'Toole
authors: Omar
authors: O
authors: Zabaneh
authors: Reza
authors: R
authors: Nourzadeh
authors: Mahmoud
authors: M
authors: Dahdouli
authors: Mostafa
authors: M
authors: Abdellateef
authors: Paul M K
authors: PM
authors: Gordon
authors: Jung
authors: J
authors: Soh
authors: Gregory
authors: G
authors: Butler
authors: Christoph W
authors: CW
authors: Sensen
authors: Adrian
authors: A
authors: Tsang
mesh_terms: D005800:Genes, Fungal; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D008390:Markov Chains; D008957:Models, Genetic; D058977:Molecular Sequence Annotation / Q000379:methods*; D012331:RNA, Fungal / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012331:RNA, Fungal