GView is a java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or as a visualization tool in a sequence annotation pipeline. Users can interact with the genome using a powerful pan-and-zoom interface, or GView can write static images of a genome to a file. GView can draw a genome using either circular or linear layouts, with additional layout types planned for future release.
Ori-Finder is an online system for finding oriCs in bacterial genomes based on an integrated method comprising the analysis of base composition asymmetry using the Z-curve method, distribution of DnaA boxes, and the occurrence of genes frequently close to oriCs. The program can also deal with the unannotated sequences by integrating the gene-finding program ZCURVE 1.02. Output of the predicted results is exported to an HTML report, which offers convenient views on the results in both graphical and tabular formats.
::DEVELOPER
TUBIC – the Tianjin University BioInformatics Centre.
PreDetector (Prokaryotic Regulatory Elements Detector) is a tool designed for biologists. Its main function is to search for the cis-elements (nucleotides) that regulate the genes for a bacteria specie, assuming that one usually consider that a cis sequence regulates a gene iff it is oriented in the same direction and if it is localised in a user-specified interval regarding to the beginning of the gene. To achieve its function, PreDetector connects to the NCBI server, which provides the information on the genes for a given bacteria. When a cis sequence is considerated as regulating a gene, PreDetector also computes the co-transcribed genes, that is the genes that are located in another user-specified interval regarding to the end of the preceding gene (and this is a recursive process). On user demand, PreDetector also allows to generate statistics containing the percentage of genic and intergenic sequences
CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome finshing process, taking advantage of the high number of near genomes that can be used to align and resolve the relative position of the contigs obtained with the latest sequencing technologies and therefore to design a set of PCR primers in order to fill the gaps and take a step further in the finishing process. It also can be used to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).
BEACON is a software tool that compares annotations of a particular genome from different Annotation Methods (AMs). It uses GenBank format as input and derives Extended Annotation (EA) along side listing original annotations from individual AMs.
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads (handles reads >500bp long). It will find both substitutions and insertions/deletions (indels).