Tag: Gene Cluster

ThioFinder 1.2 – Identification of Thiopeptide Gene Clusters in DNA sequences

ThioFinder 1.2

:: DESCRIPTION

ThioFinder is a web-based tool  to rapidly identify thiopeptide biosynthetic gene cluster from DNA sequence using a profile Hidden Markov Model approach.

::DEVELOPER

Microbial Genomics and Bioinformatics Group, SKMML, SJT

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(9):e45878. doi: 10.1371/journal.pone.0045878.
ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences.
Li J, Qu X, He X, Duan L, Wu G, Bi D, Deng Z, Liu W, Ou HY.

clinker v0.0.23 – Gene Cluster Comparison Figure Generator

clinker v0.0.23

:: DESCRIPTION

clinker is a pipeline for easily generating publication-quality gene cluster comparison figures.

::DEVELOPER

Chooi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

clinker

:: MORE INFORMATION

Citation

Gilchrist CLM, Chooi YH.
Clinker & clustermap.js: Automatic generation of gene cluster comparison figures.
Bioinformatics. 2021 Jan 18:btab007. doi: 10.1093/bioinformatics/btab007. Epub ahead of print. PMID: 33459763.

OrthoVenn2 – Comparison and Annotation of Orthologous Gene Clusters among multiple Species

OrthoVenn2

:: DESCRIPTION

OrthoVenn2 is a web platform for comparison and annotation of orthologous gene clusters among multiple species.

::DEVELOPER

OrthoVenn team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Xu L, Dong Z, Fang L, Luo Y, Wei Z, Guo H, Zhang G, Gu YQ, Coleman-Derr D, Xia Q, Wang Y.
OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species.
Nucleic Acids Res. 2019 Jul 2;47(W1):W52-W58. doi: 10.1093/nar/gkz333. PMID: 31053848; PMCID: PMC6602458.

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.
Wang Y, Coleman-Derr D, Chen G, Gu YQ.
Nucleic Acids Res. 2015 May 11. pii: gkv487.

Diametrical Clustering – Identify Anti-correlated Gene Clusters

Diametrical Clustering

:: DESCRIPTION

Diametrical clustering is a software that explicitly identifies anti-correlated clusters of genes. Our algorithm proceeds by iteratively (i) re-partitioning the genes and (ii) computing the dominant singular vector of each gene cluster; each singular vector serving as the prototype of a ‘diametric’ cluster. We empirically show the effectiveness of the algorithm in identifying diametrical or anti-correlated clusters. Testing the algorithm on yeast cell cycle data, fibroblast gene expression data, and DNA microarray data from yeast mutants reveals that opposed cellular pathways can be discovered with this method.

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Diametrical Clustering

:: MORE INFORMATION

Citation

I. S. Dhillon, E. M. Marcotte, U. Roshan,
“Diametrical Clustering for identifying anti- correlated gene clusters“,
Bioinformatics, 19, pp 1612-1619, 2003

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.

Gecko 2.0 – Gene Cluster Detection in Prokaryotic Genomes

Gecko 2.0

:: DESCRIPTION

Gecko is a further development of the original Gecko software. It allows for the systematic detection of gene cluster conservation in a large number of genomes. The enhancement over the original Gecko tool is the use of set-distance based gene cluster models that allow for the detection of gene clusters with diverse conservation patterns including gaps and missing genes in cluster occurrences. It is also tolerant of errors in gene homology assignment.

::DEVELOPER

Katharina Jahn and Leon Kuchenbecker

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

Gecko

:: MORE INFORMATION

Citation

Computation of median gene clusters
S. Böcker, K. Jahn, J. Mixtacki, and J. Stoye. J. Comp. Biol., 16(8):1085-1099, 2009.

Rococo 2.0 – Reconstruct Ancestral Gene Clusters

Rococo 2.0

:: DESCRIPTION

Rococo (Reconstruction Of Conserved Optimal Clusters of Orthologs) reconstructs ancestral gene clusters. Given the topology of a phylogenetic tree and the gene orders of the leaf nodes, it calculates sets of gene clusters for the inner nodes preserving consistency and parsimony.

::DEVELOPER

Roland Wittler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

Rococo

:: MORE INFORMATION

Citation

J. Stoye and R. Wittler,
A Unified Approach for Reconstructing Ancient Gene Clusters
IEEE/ACM Trans. Comput. Biol. Bioinf. 6(3), 387-400, 2009

clusterProfiler 3.14.0 – Statistical Analysis and Visulization of Functional Profiles for Genes and Gene Clusters

clusterProfiler 3.14.0

:: DESCRIPTION

clusterProfiler implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

::DEVELOPER

Guangchuang YU,, Li-Gen Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

  clusterProfiler

:: MORE INFORMATION

Citation

OMICS. 2012 May;16(5):284-7. doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28.
clusterProfiler: an R package for comparing biological themes among gene clusters.
Yu G1, Wang LG, Han Y, He QY.

DILTAG – Inferring the Evolutionary History of Gene Clusters from Phylogenetic and Gene Order Data

DILTAG

:: DESCRIPTION

DILTAG is an algorithm allowing to infer a set of optimal evolutionary histories for a gene cluster in a single species, according to a general cost model involving variable length duplications (in tandem or inverted), deletions, and inversions.

::DEVELOPER

NADIA EL-MABROUK

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

M. Lajoie, D. Bertrand and N. El-Mabrouk.
Inferring the Evolutionary History of Gene Clusters from Phylogenetic and Gene Order Data.
Mol Biol Evol. 2010 Apr;27(4):761-72. doi: 10.1093/molbev/msp271