Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes

Abstract

Abstract Summary: A program called Oriloc has been developed for the prediction of bacterial replication origins. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. The program works with unannotated sequences in fasta format and therefore uses glimmer 2.0 outputs to discriminate between codon positions so as to increase the signal/noise ratio. Availability: The ANSI C source code is freely available for academic use at ftp://pbil.univ-lyon1.fr/pub/logiciel/oriloc/oriloc.c. Contact: lobry@biomserv.univ-lyon1.fr Supplementary information: ftp://pbil.univ-lyon1.fr/pub/logiciel/oriloc/oriloc.ps * To whom correspondence should be addressed.