:: DESCRIPTION
RCandy is an R package for visualising homologous recombination events in bacterial genomes
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Chaguza C, Tonkin-Hill G, Lo SW, Hadfield J, Croucher NJ, Harris SR, Bentley SD.
RCandy: an R package for visualising homologous recombinations in bacterial genomes.
Bioinformatics. 2021 Dec 2:btab814. doi: 10.1093/bioinformatics/btab814. Epub ahead of print. PMID: 34864895.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Petkau A, Stuart-Edwards M, Stothard P, and Van Domselaar G.
Interactive microbial genome visualization with GView.
Bioinformatics 2010 26: 3125-3126.
:: DESCRIPTION
Bakta is a tool for the rapid & standardized annotation of bacterial genomes & plasmids.
::DEVELOPER
Bioinformatics and Systems Biology, Justus-Liebig-University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A.
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification.
Microb Genom. 2021 Nov;7(11). doi: 10.1099/mgen.0.000685. PMID: 34739369.
:: DESCRIPTION
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.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes.
Luo H, Zhang CT, Gao F.
Front Microbiol. 2014 Sep 15;5:482. doi: 10.3389/fmicb.2014.00482.
Feng Gao and Chun-Ting Zhang (2008)
Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes.
BMC Bioinformatics. 9:79.
:: DESCRIPTION
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
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hiard S, Maree R, Colson S, Hoskisson PA, Titgemeyer F, van Wezel GP, Joris B, Wehenkel L, Rigali S. (2007).
PREDetector: A new tool to identify regulatory elements in bacterial genomes.
Biochem Biophys Res Commun. 357(4):861-4.
:: DESCRIPTION
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).
::DEVELOPER
Florence Computational Biology Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Source Code Biol Med. 2011 Jun 21;6:11. doi: 10.1186/1751-0473-6-11.
CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes.
Galardini M, Biondi EG, Bazzicalupo M, Mengoni A.
:: DESCRIPTION
RNIE is a probabilistic approach for predicting RITs (Rho-independent terminators).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Aug;39(14):5845-52. doi: 10.1093/nar/gkr168. Epub 2011 Apr 7.
RNIE: genome-wide prediction of bacterial intrinsic terminators.
Gardner PP1, Barquist L, Bateman A, Nawrocki EP, Weinberg Z.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BEACON: automated tool for Bacterial GEnome Annotation ComparisON.
Kalkatawi M, Alam I, Bajic VB.
BMC Genomics. 2015 Aug 18;16(1):616. doi: 10.1186/s12864-015-1826-4.
:: DESCRIPTION
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).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Prokka is a software tool for the rapid annotation of prokaryotic genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Apr 4. [Epub ahead of print]
Prokka: rapid prokaryotic genome annotation.
Seemann T.
