DynaMIT 1.1.5 – Dynamic Motif Integration Toolkit

DynaMIT 1.1.5

:: DESCRIPTION

DynaMIT is a flexible platform for sequence and structure motifs integration, providing the means to execute multiple motif search tools, integrate their output and display the obtained results in a plethora of different ways.

::DEVELOPER

Laboratory of Translational Genomics , CIBIO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 DynaMIT

:: MORE INFORMATION

Citation

DynaMIT: the dynamic motif integration toolkit.
Dassi E, Quattrone A.
Nucleic Acids Res. 2015 Aug 7. pii: gkv807

MOST+ 1.5 – Motif Finding system combing Genomic Sequence and Heterogenous Genome-wide Signatures

MOST+ 1.5

:: DESCRIPTION

MOST+ is a fast MOTIF finding tool(MOtif finding by Suffix tree and heterogeneous Tags). It extracts distribution features of nearby epigenomic markers, like histone modification or nucleosome occupancy, to help de novo find motif, thus rendering a higher level of accuracy on characterizing motif (cross-validated by ChIP-seq data) and more co-factors.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MOST+

:: MORE INFORMATION

Citation

BMC Genomics. 2015;16 Suppl 7:S13. doi: 10.1186/1471-2164-16-S7-S13.
MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures.
Zhang Y, He Y, Zheng G, Wei C.

HTHmotif – HTH Motif Discovery

HTHmotif

:: DESCRIPTION

HTHmotif is a novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HTHmotif

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 1;26(21):2672-7. doi: 10.1093/bioinformatics/btq501. Epub 2010 Aug 31.
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.
Sahota G1, Stormo GD.

RNASampler 1.3 – Predict RNA Secondary Structure Motifs

RNASampler 1.3

:: DESCRIPTION

RNASampler is a program that predicts common RNA secondary structure motifs in a group of related sequences.RNASampler finds the common structures between two sequences by probabilistically sampling aligned stems based on stem conservation calculated from intrasequence base pairing probabilities and intersequence base alignment probabilities. It iteratively updates these probabilities based on sampled structures and subsequently recalculates stem conservation using the updated probabilities. The iterative process terminates upon convergence of the sampled structures.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

RNASampler

:: MORE INFORMATION

Citation:

Xing Xu, Yongmei Ji, and Gary D. Stormo
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
Bioinformatics, August 2007; 23: 1883 – 1891.

ALIDOT 2.0.6 – Detect Conserved Secondary Structure Motifs

ALIDOT 2.0.6

:: DESCRIPTION

ALIDOT (ALIgned DOT-plots) detects conserved secondary structure elements in relatively small sets of RNAs by combining multiple sequence alignments and secondary structure predictions. Both a (good) sequence alignment and predicted secondary structure predictions for each sequence in the alignment must be provided as inputs. alidot works either with predicted mfe structures, or with base pairing probability matrices.

The program alidot and the associated perl scripts are part of the Vienna RNA Package.

::DEVELOPER

Ivo Hofacker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ALIDOT

:: MORE INFORMATION

Citation

Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes
Ivo L. Hofacker and Peter F. Stadler
Comp & Chem., 23, 401-414 (1999)

MEME 5.0.5 – Discovering Motifs within the Sequences

MEME 5.0.5

:: DESCRIPTION

MEME (Multiple Em for Motiv Elicitation) is a tool for discovering motifs in a group of related DNA or protein sequences.A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns with variable-length gaps are split by MEME into two or more separate motifs.MEME takes as input a group of DNA or protein sequences and outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif.

MCAST searches sequences for clusters of matches to one or more nucleotide motifs

::DEVELOPER

MEME Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  MEME

:: MORE INFORMATION

Citation

MCAST: Scanning for cis-regulatory motif clusters.
Grant CE, Johnson J, Bailey TL, Noble WS.
Bioinformatics. 2015 Dec 24. pii: btv750

The MEME Suite.
Bailey TL, Johnson J, Grant CE, Noble WS.
Nucleic Acids Res. 2015 May 7. pii: gkv416.

Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble,
MEME SUITE: tools for motif discovery and searching“,
Nucleic Acids Research, 37:W202-W208, 2009

atSNP – Large-scale Testing for SNP-motif Interactions

atSNP

:: DESCRIPTION

atSNP ( Affinity Test for regulatory SNP detection ) package is a bioinformatics tool for computing and testing large-scale motif-SNP interactions.

::DEVELOPER

Chandler Zuo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R

:: DOWNLOAD

atSNP

:: MORE INFORMATION

Citation

atSNP: transcription factor binding affinity testing for regulatory SNP detection.
Zuo C, Shin S, Keleş S.
Bioinformatics. 2015 Jun 18. pii: btv328.

hfAIM – High Fidelity Autophagy-associated atg8-interacting Motifs detecting tool

hfAIM

:: DESCRIPTION

hfAIM is a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated atg8-interacting motifs in various organisms

::DEVELOPER

hfAIM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms.
Xie Q, Tzfadia O, Levy M, Weithorn E, Peled-Zehavi H, Van Parys T, Van de Peer Y, Galili G.
Autophagy. 2016 May 3;12(5):876-87. doi: 10.1080/15548627.2016.1147668.

Pscan-ChIP 1.2 – Finding Over-represented Transcription Factor-binding Site Motifs

Pscan-ChIP 1.2

:: DESCRIPTION

PscanChIP is a web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria.

::DEVELOPER

Bioinformatics Evolution @nd COmparative geNomics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PscanChIP

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.
PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
Zambelli F1, Pesole G, Pavesi G.

ExactSearch – A Fast Plant Motif Search Tool

ExactSearch

:: DESCRIPTION

ExactSearch is a web tool which enables plant biologists to search for DNA motifs in the proximal promoters, and 3′ untranslated regions of all genes from 50 genome-sequenced plant species.

::DEVELOPER

ExactSearch team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ExactSearch: a web-based plant motif search tool.
Gunasekara C, Subramanian A, Avvari JV, Li B, Chen S, Wei H.
Plant Methods. 2016 Apr 28;12:26. doi: 10.1186/s13007-016-0126-6.