ADHoRe (Automatic Detection of Homologous Regions) is a software tool that automatically detects genomic regions with statistically significant conserved gene content and order.
The ADHoRe software is freely available for academic users. Commercial users need to register for a commercial license. Please contact V.I.B license manager
Chris De Jonghe for further details.
It should be noted however that have recently published an extension of ADHoRe called i-ADHoRe. As this package also provides the same functionality as ADHoRe but is easier to use and provides clearer output you might want to consider this package instead. Click
here to go to the i-ADHoRe download page.
Vandepoele, K.,
Saeys, Y.,
Simillion, C.,
Raes, J.,
Van de Peer, Y. (2002)
The Automatic Detection of Homologous Regions (ADHoRe) and its application to microcolinearity between Arabidopsis and Rice. Genome Res. 12, 1792-801.
AFLPinSilico
performs AFLP simulations with different combinations
of restriction enzymes or selective nucleotides, on organisms
or data sets for which DNA sequences are available.
Rombauts, S.,
Van de Peer, Y.,
Rouzé, P. (2003)
AFLPInsilico, simulating AFLP fingerprints. Bioinformatics 19, 776-7.
We have developed a Java application called ASaturA that discriminates amino acid substitutions with high and low probabilities of occurrence.
Van de Peer, Y., Frickey, T., Taylor, J.S., Meyer, A. (2002)
Dealing with saturation at the amino acid level: A case study involving anciently duplicated zebrafish genes. Gene 295, 205-11.
The ATCOECIS resource makes it possible to query coexpression data, GO and cis-regulatory elements annotations, submit user-defined gene
sets for motif analysis and provides an access point to unravel the regulatory code underlying transcriptional control in Arabidopsis.
Matlab toolbox to compute DNA melting properties using a helicoidal transfer matrix model.
Michoel, T.,
Van de Peer, Y. (2006)
A helicoidal transfer matrix model for inhomogeneous DNA melting. Physical Review E. 73, 011908.
ENIGMA is a software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating GO annotation and transcription factor binding information and by learning tentative regulation programs.
EP3 is a tool for the identification of the core region of a eukaryotic gene promoter. It uses universal properties of the promoter to detect those regions in a whole genome context. EP3 has been tested on several eukaryotes ranging from protists to human. On human it is, at the moment, the best performing tool to identify regions that are associated with transcription initiation.
Abeel, T.,
Van de Peer, Y.,
Saeys, Y. (2009)
Towards a gold standard for promoter prediction evaluation. Bioinformatics 25, i313-i320.
An open source gene finder to annotate eukaryotic sequences
Foissac, S., Gouzy, J.P.,
Rombauts, S., Mathé, C., Amselem, J.,
Sterck, L.,
Van de Peer, Y.,
Rouzé, P., Schiex, T. (2008)
Genome Annotation in Plants and Fungi: EuGene as a model platform. Current Bioinformatics 3, 87-97.
ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments.
Raes, J.,
Van de Peer, Y. (1999)
ForCon : a software tool for the conversion of sequence alignments. Embnet. News 6, 10-12..
FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA
Van Bel, M.,
Saeys, Y.,
Van de Peer, Y. (2008)
FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA. Bioinformatics 24, 1532-3.
GaneSh - a software to cluster expression data by Gibbs sampling procedure
Joshi, A.,
Van de Peer, Y.,
Michoel, T. (2008)
Analysis of a Gibbs sampler method for model based clustering of gene expression data. Bioinformatics 24, 176-83.
HYPERbolic phyloGENY viewer allows hyperbolic visualisation of very large tree structures. Both an online and offline version is available.
i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.
The i-ADHoRe software is freely available for academic users. Commercial users need to register for a commercial license. Please contact V.I.B license manager
Chris De Jonghe for further details.
Simillion, C., Janssens, K.,
Sterck, L.,
Van de Peer, Y. (2008)
i-ADHoRe 2.0: An improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics 24, 127-8.
Java package for learning module networks from gene expression data.
MatrixClust is a Matlab toolbox for fuzzy clustering of a symmetric matrix, typically the weighted adjacency matrix of an undirected network. The algorithm is an improved version of the fuzzy clustering algorithm described in
Joshi, A.,
Van de Peer, Y.,
Michoel, T. (2008)
Analysis of a Gibbs sampler method for model based clustering of gene expression data. Bioinformatics 24, 176-83.
The Network Notif Clustering Toolbox is a
toolbox for clustering topological network motifs in large-scale,
integrated networks.
The Cytoscape plug-in ‘Pathicular’ identifies path motifs in integrated networks and arranges them in a modular structure. After the
integrated network and the source network (deletion
or overexpression in this case) are loaded into Cytoscape, Pathicular can be used to find all the paths
of a given type in the source network using the integrated network. A p-value is provided to check the
overrepresentation of the path of interest.
We present a large-scale benchmarking study of 17 state-of-the-art PPPs.
Abeel, T.,
Van de Peer, Y.,
Saeys, Y. (2009)
Towards a gold standard for promoter prediction evaluation. Bioinformatics 25, i313-i320.
ProSOM is a promoter prediction program based on unsupervised clustering of physical properties of DNA. The program can clearly distinguish between the structural
profiles of promoter sequences and other genomic sequences by using self-organizing maps.
Abeel, T.,
Saeys, Y.,
Rouzé, P.,
Van de Peer, Y. (2008)
ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics 24, i24-i31.
This is RANDFOLD version 2. The software compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.
*
Bonnet, E., *
Wuyts, J.,
Rouzé, P.,
Van de Peer, Y. (2004)
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20, 2911-7.
*contributed equally
SPADS (Specific Primer and Amplicon Design Software) is a tool for the design of specific GSTs (Gene Specific Tags).
A splice site prediction tool named SpliceMachine that
- shows state-of-the-art prediction performance on Arabidopsis thaliana and human sequences,
- performs a computationally fast annotation and
- can be trained by the user on its own data.
Degroeve, S.,
Saeys, Y., De Baets, B.,
Rouzé, P.,
Van de Peer, Y. (2005)
Predicting splice sites from high-dimensional local context representations. Bioinformatics 21, 1332-8.
StartScan is a tool to detect translation initiation sites (TIS) in genomic sequences. Due to its efficient
design, StartScan shows state-of-the-art performance on genome wide TIS detection, while at the same
time being a fast annotation tool. So far, the model only works for Human, but models for other organisms
can be trained upon request.
Saeys, Y.,
Abeel, T.,
Degroeve, S.,
Van de Peer, Y. (2007)
Translation initiation site prediction on a genomic scale: beauty in simplicity. Bioinformatics 23, 418-23.
TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences.
Van de Peer, Y., De Wachter, Y. (1994)
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Applic. Biosci. 10, 569-70.
This package contains 3 small programs to convert phylogenetic trees
between NH, NHX and Treecon formats.
These 3 programs are implemented as TCL (http://www.tcl.tk/) scripts.
TCL is installed by default on most Unix systems (Linux, MacOS X,
Solaris,...). Windows users will first need to install TCL.
ZT is a free software tool which performs simple and partial Mantel tests.
Bonnet, E.,
Van de Peer, Y. (2002)
ZT: a software tool for simple and partial Mantel tests. J. Stat. Soft. 7, 1-12..
