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.

Pscan 1.4 – MOtif Discovery in Nucleotide Sequences from Co-regulated Genes

Pscan 1.4

:: 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.

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.

BLSSPELLER 1.0 – Exhaustive Comparative Motif Discovery

BLSSPELLER 1.0

:: DESCRIPTION

The BLSSpeller software provides 3 main functionalities to the user: de novo comparative motif discovery, pattern matching (with BLS cutoff) and target prediction.

::DEVELOPER

Dieter De Witte Email: dieter.dewitte@intec.ugent.be

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BLSSpeller

:: MORE INFORMATION

Citation:

De Witte D, Van De Velde J, Decap D, Van Bel M, Audenaert P, Demeester P, Dhoedt B, Vandepoele K, Fostier J.
BLSSpeller: Exhaustive comparative motif discovery of conserved cis-regulatory elements.
Bioinformatics. 2015 Aug 8. pii: btv466.

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.

BayesMotif 1.0 – Sorting Motif Discovery using Bayes Classifiers

BayesMotif 1.0

:: DESCRIPTION

BayesMotif is a de novo identification algorithm for finding a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions.

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S66. doi: 10.1186/1471-2105-11-S1-S66.
BayesMotif: de novo protein sorting motif discovery from impure datasets.
Hu J1, Zhang F.

MITSU 1.0 – Stochastic EM for Transcription Factor Binding Site Motif Discovery

MITSU 1.0

:: DESCRIPTION

MITSU (Motif discovery by ITerative Sampling and Updating) is a command line application for the discovery of transcription factor binding site (TFBS) motifs.

::DEVELOPER

Alastair M Kilpatrick

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows
  • Java
  • BioJava

:: DOWNLOAD

 MITSU

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i310-i318. doi: 10.1093/bioinformatics/btu286.
Stochastic EM-based TFBS motif discovery with MITSU.
Kilpatrick AM, Ward B, Aitken S.