MultiGeneBlast 1.1.14 – Combined BLAST searches for Operons and Gene Clusters

MultiGeneBlast 1.1.14

:: DESCRIPTION

MultiGeneBlast is an open source tool for identification of homologs of multigene modules such as operons and gene clusters. It is based on a reformatting of the FASTA headers of NCBI GenBank protein entries, using which it can track down their source nucleotide and coordinates.

::DEVELOPER

MultiGeneBlast team

:: SCREENSHOTS

MultiGeneBlast

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 MultiGeneBlast

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 May;30(5):1218-23. doi: 10.1093/molbev/mst025. Epub 2013 Feb 14.
Detecting sequence homology at the gene cluster level with MultiGeneBlast.
Medema MH1, Takano E, Breitling R.

LOCP – Locating Pilus Operons in Gram-positive Bacteria

LOCP

:: DESCRIPTION

LOCP is designed to LOCate putative Pilus operons in Gram-positive prokaryotes. This is done in two steps: First, pilus-related sequences are identified by hmmsearch with a carefully selected set of profile Hidden Markov Models (HMM). Each protein sequence is then labeled either with the matching HMM models, or with the null-model, if the maximum bit score of all matches is below zero. Sequences labeled with HMMs are referred as hits and those labeled with null-model as gaps. Second, chromosome regions with statistically significant clustering of hits are located using hypergeometrical distribution and Monte Carlo simulations. These regions are referred as Pilus Like Dense Regions (PLDRs).

::DEVELOPER

Liisa Holm’s Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 LOCP

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 May 1;25(9):1187-8. doi: 10.1093/bioinformatics/btp127. Epub 2009 Mar 4.
LOCP–locating pilus operons in gram-positive bacteria.
Plyusnin I1, Holm L, Kankainen M.

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.

UNIPOP 0.1 – UNIversal Predictor of OPerons

UNIPOP 0.1

:: DESCRIPTION

UNIPOP cantains 365 predicted genome-scale operons.

::DEVELOPER

Che Lab of Bioinformatics at ESU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  UNIPOP

:: MORE INFORMATION

Citation

G. Li, Dongsheng Che and Y. Xu.
A Universal and Accurate Operon Predictor for All Prokaryotic Genomes.
Journal of Bioinformatics and Computational Biology, 7(1):19-38

OperonDT 0.1 – Operon Predictor using Decision Tree Approach

OperonDT 0.1

:: DESCRIPTION

OperonDT is an operon predictor using decision tree approach. OperonDT mainly uses three kinds of features: intergenic distance, COG pattern and gene order conservation to build tree models.

::DEVELOPER

Che Lab of Bioinformatics at ESU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OperonDT

:: MORE INFORMATION

Citation

Decision tree modeling predicts operon structures of prokaryotic genomes
Dongsheng Che, J. Zhao, L. Cai, Y. Xu
International Journal of Information Technology and Intelligent Computing, (2007), 2(1)

PMAP II – Resolve pathway mapping problem with Operon and Regulon information

PMAP II

:: DESCRIPTION

P-MAP is an software for resolving pathway mapping problem with Operon and Regulon information.

PMAP Online Version

::DEVELOPER

the Computational Systems Biology Laboratory at the University of Georgia 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PMAP

:: MORE INFORMATION

Citation

F. Mao, Z. Su, V. Olman, P. Dam, Z. Liu, Ying Xu,
Mapping of orthologous genes in the context of biological pathways: an application of integer programming“,
Proc Natl Acad Sci USA, 103 (1): 129-134, 2006.