ReviSeq 0.1.2 – Revising Bacterial Genome Sequences

ReviSeq 0.1.2

:: DESCRIPTION

ReviSeq is a free tool to generate and to revise a bacterial genome sequence from short sequence reads and a reference sequence.

::DEVELOPER

ReviSeq team

:: SCREENSHOTS

Command

:: REQUIREMENTS

:: DOWNLOAD

 ReviSeq

 :: MORE INFORMATION

Citation:

Genomics. 2012 Nov;100(5):271-6. doi: 10.1016/j.ygeno.2012.07.015. Epub 2012 Aug 10.
Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes.
Tae H, Settlage RE, Shallom S, Bavarva JH, Preston D, Hawkins GN, Adams LG, Garner HR.

BPhyOG 1.0 – Bacterial Phylogenies based on Overlapping Genes

BPhyOG 1.0

:: DESCRIPTION

BPhyOG is an interactive web server for reconstruction of whole-genome bacterial phylogenies based on overlapping genes, and also allows users to browse overlapping genes to acquire more information about subtree-specific genomes or all the 177 genomes.

:: DEVELOPER

Laboratory of Computational Molecular Biology, Beijing Normal University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BPhyOG: an interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes.
Luo Y, Fu C, Zhang DY, Lin K.
BMC Bioinformatics. 2007 Jul 25;8:266.

AMPHORA2 – Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences

AMPHORA2

:: DESCRIPTION

AMPHORA is an automated phylogenomic inference application for large-scale protein phylogenetic analysis. It has been applied to automated genome tree construction and metagenomic sequence phylotyping.

::DEVELOPER

Wu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AMPHORA2

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 1;28(7):1033-4. doi: 10.1093/bioinformatics/bts079. Epub 2012 Feb 12.
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.
Wu M1, Scott AJ.

Barrnap 0.9 – Bacterial ribosomal RNA predictor

Barrnap 0.9

:: DESCRIPTION

Barrnap predicts the location of 5S, 16S and 23S ribosomal RNA genes in Bacterial genome sequences. It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1-dev for HMM searching in DNA:DNA style

::DEVELOPER

Torsten Seemann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • NHMMER

:: DOWNLOAD

 Barrnap

:: MORE INFORMATION

MFlux – Rapid Prediction of Bacterial Heterotrophic Fluxomics

MFlux

:: DESCRIPTION

MFlux is a web-based platform that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms.

::DEVELOPER

MFlux team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming.
Wu SG, Wang Y, Jiang W, Oyetunde T, Yao R, Zhang X, Shimizu K, Tang YJ, Bao FS.
PLoS Comput Biol. 2016 Apr 19;12(4):e1004838. doi: 10.1371/journal.pcbi.1004838.

OpWise – Operons Aid the Identification of differentially Expressed Genes in Bacterial Microarray Experiments

OpWise

:: DESCRIPTION

To estimate the reliability of bacterial microarray experiments, OpWise uses the agreement of measurements within operons to estimate the amount of systematic bias in the data. OpWise relies on the MicrobesOnline operons predictions.

::DEVELOPER

Morgan N. PriceAdam P. Arkin, and Eric J. Alm

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R package

:: DOWNLOAD

 OpWise

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Jan 13;7:19.
OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments.
Price MN, Arkin AP, Alm EJ.

CoBaltDB 1.0 – Complete Bacterial and Archaeal Orfeomes Subcellular Localization Database

CoBaltDB 1.0

:: DESCRIPTION

CoBaltDB (Complete Bacterial and Archaeal Orfeomes Subcellular Localization Database) which aims at presenting the cellular localisation of all prokaryotic proteins of all sequenced genomes, as predicted by numerous bioinformatic localisation tools.

::DEVELOPER

B@SIC (Bioinformatics Applied to Stresses and Cellular Interactions)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac / Linux
  • Java

:: DOWNLOAD

  CoBaltDB

:: MORE INFORMATION

Citation

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources.
Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F.
BMC Microbiol. 2010 Mar 23;10:88.