Prodigal: prokaryotic gene recognition and translation initiation site identification View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-12

AUTHORS

Doug Hyatt, Gwo-Liang Chen, Philip F LoCascio, Miriam L Land, Frank W Larimer, Loren J Hauser

ABSTRACT

BACKGROUND: The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. RESULTS: With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. CONCLUSION: We built a fast, lightweight, open source gene prediction program called Prodigal http://compbio.ornl.gov/prodigal/. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines. More... »

PAGES

119

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-11-119

DOI

http://dx.doi.org/10.1186/1471-2105-11-119

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1026423599

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/20211023


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