:: DESCRIPTION
Wombac rapidly finds core genome SNPs from samples and produces an alignment of those SNPs which can be used to build a phylogenomic tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
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.
::DEVELOPER
Laboratory of Bioinformatics Analyses for Genomics and Metabolism ( LABGeM )
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W471-9.
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.
Cruveiller S, Le Saux J, Vallenet D, Lajus A, Bocs S, Médigue C.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Syst Biol. 2019 Feb 22;15(2):e8290. doi: 10.15252/msb.20188290.
Unraveling the hidden universe of small proteins in bacterial genomes.
Miravet-Verde S, Ferrar T, Espadas-García G, Mazzolini R, Gharrab A, Sabido E, Serrano L, Lluch-Senar M.
:: DESCRIPTION
BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.
::DEVELOPER
the Wishart Research Group, University of Alberta
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
BASys: a web server for automated bacterial genome annotation.
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W455-9.
:: DESCRIPTION
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.
::DEVELOPER
Dr. Derrick E. Fouts at J. Craig Venter Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Derrick E. Fouts
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences
Nucl. Acids Res. (2006) 34 (20): 5839-5851.doi: 10.1093/nar/gkl732
:: DESCRIPTION
ArrayOme is a new software system to predict the size of the microarray-visualised genome (MVG) based on microarray-derived comparative genomic hybridization data.
::DEVELOPER
Hong-Yu Ou (tjohy@hotmail.com)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hong-Yu Ou et al.
ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes
Nucl. Acids Res. (2005) 33 (1): e3.
:: DESCRIPTION
PILER is public domain software for analyzing repetitive DNA found in genome sequences.The PILER algorithm was developed by Bob Edgar and Gene Myers.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
PILER-CR Source Code ; for mac
:: MORE INFORMATION
Citation
R.C. Edgar and E.W. Myers
PILER: identification and classification of genomic repeats.
Bioinformatics. 2005 Jun 1;21 Suppl 1:i152-i158