sMotif / exMotif – Extract / Mine Structured Sequence Motifs DNA sequences

sMotif / exMotif

:: DESCRIPTION

sMotif and exMotif are two complementary for searching and extracting/mining structured sequence motifs DNA sequences. A structured motif consists of simple motifs separated by different gap lengths. The simple motif may be a simple pattern or a position weighted matrix or profile. Given a template structured motif (pattern or profile), sMotif finds all matches in a given set of sequences. On the other hand, exMotif mines novel motifs matching some minimal conditions on the gaps and frequency.

::DEVELOPER

Mohammed J. Zaki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 sMotif / exMotif

:: MORE INFORMATION

Citation

Yongqiang Zhang and Mohammed J. Zaki,
EXMOTIF: efficient structured motif extraction.
Algorithms for molecular biology, 1(21). Nov 2006.

Yongqiang Zhang and Mohammed J. Zaki,
SMOTIF: efficient structured pattern and profile motif search.
Algorithms for molecular biology, 1(22). Nov 2006.

HMS 0.1 – Hybrid Motif Sampler

HMS 0.1

:: DESCRIPTION

HMS (hybrid motif sampler) implements a novel computational algorithm specifically designed for transcription factor binding sites (TFBS) motif discovery using ChIP-Seq data. HMS combines stochastic sampling with determinstic greedy search to achieve rapid and accurate motif pattern identification. In addition, it can identify non-ignorable inter-position dependency inside TFBS motifs.

::DEVELOPER

Ming Hu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HMS

:: MORE INFORMATION

Citation

Hu M, Yu J, Taylor JM, Chinnaiyan AM, Qin ZS.
On the detection and refinement of transcription factor binding sites using ChIP-Seq data.
Nucleic Acids Res. 2010 Apr;38(7):2154-67. Epub 2010 Jan 6.

DIAL – 3-Dimensional RNA Structural Alignment and Motif Detection

DIAL

:: DESCRIPTION

DIAL is a web server for 3-dimensional RNA structural alignment (global and local) and for motif detection. DIAL (DIhedral ALignment) runs in time that is quadratic in input length by performing an alignment which accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity, (iii) nucleotide base-pairing similarity.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

DIAL

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

F. Ferre; Y. Ponty; W. A. Lorenz; Peter Clote
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities ,
Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W659-68. Epub 2007 Jun 13.

Gibbs Motif Sampler 3.2 – Identify Motifs, Conserved Regions, in DNA or Protein Sequences

Gibbs Motif Sampler 3.2

:: DESCRIPTION

The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences.

::DEVELOPER

Wadsworth Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows with Cygwin/MacOsX

:: DOWNLOAD

 Gibbs Motif Sampler

:: MORE INFORMATION

Citation

Neuwald AF, Liu JS, and Lawrence CE. (1995)
Gibbs motif sampling: detection of bacterial outer membrane protein repeats.
Protein Sci 4(8):1618-1632. PubMed: 8520488.

Haystack 0.5.5 – Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Haystack 0.5.5

:: DESCRIPTION

Haystack is a suite of computational tools implemented in a Python 2.7 package called haystack_bio to study epigenetic variability, cross-cell-type plasticity of chromatin states and transcription factors (TFs) motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

Haystack

:: MORE INFORMATION

Citation

Bioinformatics, 34 (11), 1930-1933 2018 Jun 1
Haystack: Systematic Analysis of the Variation of Epigenetic States and Cell-Type Specific Regulatory Elements
Luca Pinello, Rick Farouni, Guo-Cheng Yuan

MIM – Motif Independent Metric

MIM

:: DESCRIPTION

MIM calculates a measure of sequence specificity called Motif Independent Metric.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

 MIM 

:: MORE INFORMATION

Citation

A motif-independent metric for DNA sequence specificity.
Pinello L, Lo Bosco G, Hanlon B, Yuan GC.
BMC Bioinformatics. 2011 Oct 21;12:408.

MAVisto 2.7.0 – Motif Analysis and VISualisation TOolkit

MAVisto 2.7.0

:: DESCRIPTION

MAVisto (Motif Analysis and VISualisation TOolkit)is a tool for the exploration of motifs in network. It provides a flexible motif search algorithm and different views for the analysis and visualisation of network motifs.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 MAVisto

:: MORE INFORMATION

Citation

Schreiber, F. and Schwöbbermeyer H.
MAVisto: a tool for the exploration of network motifs.
Bioinformatics, 21, 3572-3574, 2005.

p53scan 1.05 & p63scan – Search for the p53 or p63 Motif

p53scan 1.05 & p63scan

:: DESCRIPTION

p53scan is an algorithm to search for p53 consensus binding motif, as determined in a genome-wide ChIP-chip study, in DNA sequences. The same algorithm has also been combined with the p63 binding motif obtained from a genome-wide p63 ChIP-seq study in human keratinocytes to form p63scan.

::DEVELOPER

p53scan team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • C Compiler
  • Python

:: DOWNLOAD

 p53scan

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jun;36(11):3639-54. doi: 10.1093/nar/gkn232. Epub 2008 May 12.
Characterization of genome-wide p53-binding sites upon stress response.
Smeenk L, van Heeringen SJ, Koeppel M, van Driel MA, Bartels SJ, Akkers RC, Denissov S, Stunnenberg HG, Lohrum M.

Kouwenhoven EN, van Heeringen SJ, Tena JJ, Oti M, Dutilh BE et al.
Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.
PLoS Genet. 2010 Aug 19;6(8):e1001065. doi: 10.1371/journal.pgen.1001065.

GimmeMotifs 0.14.2 – Systematic de novo Motif Prediction pipeline

GimmeMotifs 0.14.2

:: DESCRIPTION

GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.

::DEVELOPER

van Heeringen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GimmeMotifs

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):270-1. doi: 10.1093/bioinformatics/btq636. Epub 2010 Nov 15.
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments.
van Heeringen SJ, Veenstra GJ.