ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes

• DOI: 10.1093/bioinformatics/btw393
• Publication Date: 2016-07-05T01:59:34Z
• Authors: Thomas Weinmaier; Alexander Platzer; Jeroen Frank; Hans-Jörg Hellinger; Patrick Tischler; Thomas Rattei
• Keywords: Perl; Gene Annotation; Gene prediction; MIT License

Abstract Motivation: The rapidly growing number of available prokaryotic genome sequences requires fully automated and high-quality software solutions for their initial re-annotation. Here we present ConsPred, a annotation framework that performs intrinsic gene predictions, homology searches, predictions non-coding genes as well CRISPR repeats integrates all evidence into consensus annotation. ConsPred achieves comprehensive, annotations based on rules priorities, similar to decision-making in manual curation avoids conflicting predictions. Parameters controlling the process are configurable by user. has been used institutions authors longer than 5 years can easily be extended adapted specific needs. Summary: algorithm producing from varying scores multiple prediction programs approaches accuracy. Its rule-based approach choosing final overriding previous curations. Availability implementation: is implemented Java, Perl Shell freely under Creative Commons license stand-alone in-house pipeline or an Amazon Machine Image cloud computing, see https://sourceforge.net/projects/conspred/. Contact: [e-mail] Supplementary information: data at Bioinformatics online.