Prophinder: a computational tool for prophage prediction in prokaryotic genomes
Open Access
- 30 January 2008
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 24 (6) , 863-865
- https://doi.org/10.1093/bioinformatics/btn043
Abstract
Summary: Prophinder is a prophage prediction tool coupled with a prediction database, a web server and web service. Predicted prophages will help to fill the gaps in the current sparse phage sequence space, which should cover an estimated 100 million species. Systematic and reliable predictions will enable further studies of prophages contribution to the bacteriophage gene pool and to better understand gene shuffling between prophages and phages infecting the same host. Availability: Softare is available at http://aclame.ulb.ac.be/prophinder Contact:gipsi@scmbb.ulb.ac.be Supplementary information: Supplementary data is available on http://aclame.ulb.ac.be/Tools/Prophinder/evaluations_table.html.Keywords
This publication has 6 references indexed in Scilit:
- Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequencesNucleic Acids Research, 2006
- ACLAME: A CLAssification of Mobile genetic ElementsNucleic Acids Research, 2004
- Prophages and bacterial genomics: what have we learned so far?Molecular Microbiology, 2003
- Global Phage DiversityCell, 2003
- Evolutionary relationships among diverse bacteriophages and prophages: All the world’s a phageProceedings of the National Academy of Sciences, 1999
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997