BayesMD – Biological Modeling for Motif Discovery

BayesMD

:: DESCRIPTION

BayesMD is a flexible, fully Bayesian model for motif discovery consisting of motif, background and alignment modules. BayesMD can be customized to different kind of biological applications, e.g. microarray, ChIP-chip, ditag, CAGE data analysis by integrating appropriately chosen features and functionalities.

::DEVELOPER

BayesMD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Matlab

:: DOWNLOAD

  BayesMD

:: MORE INFORMATION

Citation:

J Comput Biol. 2008 Dec;15(10):1347-63. doi: 10.1089/cmb.2007.0176.
BayesMD: flexible biological modeling for motif discovery.
Tang MH, Krogh A, Winther O.

Varun – Extensible Motif Discovery

Varun

:: DESCRIPTION

Varun is suite of software programs implementing the discovery of extensible motifs of the type considered.

::DEVELOPER

ALBERTO APOSTOLICO , Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Varun

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):752-26. doi: 10.1109/TCBB.2008.123.
VARUN: discovering extensible motifs under saturation constraints.
Apostolico A, Comin M, Parida L.

Pscan 1.5 – MOtif Discovery in Nucleotide Sequences from Co-regulated Genes

Pscan 1.5

:: DESCRIPTION

Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences. Pscan does not resort to comparisons with orthologous sequences and experimental results show that it compares favorably to other tools for the same task in terms of false positive predictions and computation time.

::DEVELOPER

Bioinformatics Evolution @nd COmparative geNomics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Pscan

:: MORE INFORMATION

Citation:

F.Zambelli, G.Pesole, G.Pavesi
Pscan: Finding Over-represented Transcription Factor Binding Site Motifs in Sequences from Co-Regulated or Co-Expressed Genes.
Nucleic Acids Research 2009 37(Web Server issue):W247-W252.

Weeder 2.0 / WeederH 1.0 – Motif Discovery in Sequences from Coregulated Genes of a Single Species

Weeder 2.0 / WeederH 1.0

:: DESCRIPTION

Weeder is an algorithm for the automatic discovery of conserved motifs in a set of related regulatory DNA sequences.

WeederH is a software for finding of conserved nucleotide motifs and regions through comparative genomics, tailored for the analysis of non-coding DNA and the identification of conserved TFBSs or whole enhancers or silencers.

::DEVELOPER

the Research Network of Bioinformatics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Weeder / WeederH

:: MORE INFORMATION

Citation:

Pavesi, G., Mereghetti, P., Mauri, G. and Pesole, G. (2004)
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.
Nucleic Acids Res., 32, W199-203.

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.
Pavesi G, Zambelli F, Pesole G.
BMC Bioinformatics. 2007 Feb 7;8:46.

Allegro 1.0 / Amadeus 1.2 – Motif Discovery Platform

Allegro 1.0 / Amadeus 1.2

:: DESCRIPTION

Allegro is a software tool for simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). Allegro is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.

Amadeus is a user-friendly software platform for genome-scale detection of known and novel motifs (recurring patterns) in DNA sequences, applicable to a wide range of motif discovery tasks. Amadeus outperforms extant tools and sets a new standard for motif discovery software in terms of accuracy, running time, range of application, wealth of output information and ease of use.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 Allegro / Amadeus

:: MORE INFORMATION

Citation

Allegro: Analyzing expression and sequence in concert to discover regulatory programs“,
Y. Halperin, C. Linhart, I. Ulitsky and R. Shamir,
Nucleic Acids Research, vol. 37:5, pp. 1566-1579, April 2009.

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets“,
C. Linhart, Y. Halperin and R. Shamir,
Genome Research, vol. 18:7, pp. 1180-1189, July 2008.

PhyloNet v2b – Motif Discovery at Whole Genome Level

PhyloNet v2b

:: DESCRIPTION

PhyloNet (Phylogenetic Regulatory Network) is a motif discovery program.  It represents a very new paradigm for motif discovery: based on sequences of several evolutionarily related genomes, PhyloNet predicts a near complete set of conserved motifs of the organism of interest,as well as gene clusters that share these motifs, without reliance of additional data such as gene regulation.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhyloNet

:: MORE INFORMATION

Zagros 1.1.0 – Motif discovery using CLIP-Seq data

Zagros 1.1.0

:: DESCRIPTION

Zagros is a motif discovery software for CLIP-Seq high-throughput protein-RNA interaction data. Given the regions of significant enrichment for reads Zagros can characterize the binding site for the given RBP. Zagros contains two additional programs to calculate the base pairing probabilities of the input sequences and extracting experiment specific events to incorporate such information for an extremely accurate motif discovery.

::DEVELOPER

The Smith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Zagros

:: MORE INFORMATION

Citation

Leveraging cross-link modification events in CLIP-seq for motif discovery.
Bahrami-Samani E, Penalva LO, Smith AD, Uren PJ.
Nucleic Acids Res. 2015 Jan;43(1):95-103. doi: 10.1093/nar/gku1288.

XXmotif 1.6 – eXhaustive, weight matriX-based Motif Discovery in Nucleotide Sequences

XXmotif 1.6

:: DESCRIPTION

The XXmotif web server can discover motifs that are enriched in sets of nucleotide sequences provided by the user. XXmotif uses a new approach for finding enriched motifs: It directly optimizes the statistical significance of enrichment for PWMs. It can also score conservation and positional clustering of motifs. In several benchmarks on yeast and metazoan sequences, the underlying XXmotif method showed better sensitivity and produced PWMs of higher quality than state-of-the-art tools.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl

:: DOWNLOAD

 XXmotif

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W104-9. doi: 10.1093/nar/gks602. Epub 2012 Jun 12.
The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences.
Luehr S, Hartmann H, Söding J.

CUDA-MEME 2.74 / mCUDA-MEME 3.0.16 – Motif Discovery software based on MEME

CUDA-MEME 2.74 / mCUDA-MEME 3.0.16

:: DESCRIPTION

CUDA-MEME is a motif discovery software based on MEME   algorithm for a single GPU device using CUDA programming model. At present, CUDA-MEME only supports the OOPS and ZOOPS models.

mCUDA-MEME is a further extension of CUDA-MEME based on MEME algorithm for mutliple GPUs using a hybrid combination of CUDA, MPI and OpenMP.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA toolkits and SDK 2.0 or higher.

:: DOWNLOAD

   CUDA-MEME / mCUDA-MEME

:: MORE INFORMATION

Citation:

Yongchao Liu, Bertil Schmidt, Weiguo Liu, Douglas L. Maskell:
CUDA-MEME: accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units“.
Pattern Recognition Letters, 2010, 31(14): 2170 – 2177

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
An ultrafast scalable many-core motif discovery algorithm for multiple GPUs“.
10th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2011), 2011, 428-434

W-ChIPMotifs – de novo Motif Discovery from ChIP-based High throughput data

W-ChIPMotifs

:: DESCRIPTION

W-ChIPMotifs is a web application tool for de novo motif discovery from ChIP-based high throughput data.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data.
Jin VX, Apostolos J, Nagisetty NS, Farnham PJ.
Bioinformatics. 2009 Dec 1;25(23):3191-3.