MICheck (Microbial Genome checker), is a web software enables rapid verification of sets of annotated genes and frameshifts (syntaxic annotation), in complete bacterial genomes that are available in public databanks.
RanSEPs (a random forest‐based tool for the prediction of SEPs in any bacterial genome)provides a framework for bacterial genome re-annotation and novel small proteins (SEPs) detection adjusting the search to different genomic features that govern protein-coding capabilities.
BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.
Phage_Finder, a heuristic computer program, was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, Phage_Finder found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. A search of 302 complete bacterial genomes predicted 403 putative prophage regions, accounting for 2.7% of the total bacterial DNA. Analysis of the 285 putative attachment sites revealed tRNAs are targets for integration slightly more frequently (33%) than intergenic (31%) or intragenic (28%) regions, while tmRNAs were targeted in 8% of the regions. The most popular tRNA targets were Arg, Leu, Ser and Thr. Mapping of the insertion point on a consensus tRNA molecule revealed novel insertion points on the 5′ side of the D loop, the 3′ side of the anticodon loop and the anticodon. A novel method of constructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST score ratio (BSR) of the phage/prophage proteomes.
ArrayOme is a new software system to predict the size of the microarray-visualised genome (MVG) based on microarray-derived comparative genomic hybridization data.