sTarPicker – Global Target Prediction for Bacterial small non-coding RNAs

sTarPicker

:: DESCRIPTION

sTarPicker is a novel method for sRNA target prediction which was based on a two-step model for hybridization between an sRNA and an mRNA target.

::DEVELOPER

Prof. Wuju Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 sTarPicker

:: MORE INFORMATION

Citation:

PLoS One. 2011;6(7):e22705. doi: 10.1371/journal.pone.0022705. Epub 2011 Jul 22.
sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization.
Ying X1, Cao Y, Wu J, Liu Q, Cha L, Li W.

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.

Barrnap 0.7 – Bacterial ribosomal RNA predictor

Barrnap 0.7

:: 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 <torsten.seemann@monash.edu>,Victorian Bioinformatics Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • NHMMER

:: DOWNLOAD

 Barrnap

:: MORE INFORMATION

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.

SeqTU r12 – Bacterial RNA-Seq analysis to Identify Transcription Units (TUs)

SeqTU r12

:: DESCRIPTION

SeqTU is a software of analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum

::DEVELOPER

SeqTU team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
:: DOWNLOAD

 SeqTU

:: MORE INFORMATION

Citation

Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum.
Chou WC, Ma Q, Yang S, Cao S, Klingeman DM, Brown SD, Xu Y.
Nucleic Acids Res. 2015 Mar 12. pii: gkv177.

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.

BACMan 2.1 – Bacterial Artificial Chromosome Data Management

BACMan 2.1

:: DESCRIPTION

BACMan is a Microsoft Access based application designed for the management and analysis of hybridization data related to the high throughput screening of large insert genomic libraries associated with physical mapping projects. BACMan integrates information from the entire process involved in BAC based hybridization screening so that final hybridization data are tractable through individual autoradiographs, probe preparation, and gridding of the blots used in the experiment. All BAC library plates and autoradiographs are indexed using a barcode system both to facilitate this data tracking and to ensure quality control. This barcode system also allows for computer-assisted scoring of autoradiographs and therefore increases the potential throughput of an individual user. BACMan also facilitates the design and deconvolution of pooled probe multiplexed experiments to maximize data generation, and allows for interoperability with FPC.

::DEVELOPER

James C. Estill

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • MS Access,
  • MySQL
  • Visual Basic for Applications
  • Visual Basic.Net

:: DOWNLOAD

 BACMan

:: MORE INFORMATION

sRNATarget 2.0 – Prediction of Bacterial sRNA Targets

sRNATarget 2.0

:: DESCRIPTION

sRNATarget is a webserver for sRNA target mRNA prediction.

::DEVELOPER

Prof. Wuju Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

sRNATarget: a web server for prediction of bacterial sRNA targets.
Cao Y, Zhao Y, Cha L, Ying X, Wang L, Shao N, Li W.
Bioinformation. 2009 Apr 29;3(8):364-6.

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

Garner Lab

:: 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.

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.