MEME 4.11.2 – Discovering Motifs within the Sequences

MEME 4.11.2

:: 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

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.

motifDiverge 0.4.12 — Motif Divergence between Sequence Pairs

motifDiverge 0.4.12

:: DESCRIPTION

motifDiverge is a software package implementing a statistical model for regulatory divergence based on transcription factor binding site motifs.

::DEVELOPER

Kostka Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R

:: DOWNLOAD

 motifDiverge

:: MORE INFORMATION

Citation

motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences.
D Kostka, T Friedrich, AK Holloway, KS Pollard 2014,
(under review / in revison).

STEME 1.9.1 – Motif Finder for large data sets

STEME 1.9.1

:: DESCRIPTION

STEME is a suite of Python programs to perform fast analysis of sequence motifs suitable for the huge sequence datasets available from short read sequencing.

::DEVELOPER

Statistical Bioinformatics Programme,MRC Biostatistics Unit

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python

:: DOWNLOAD

 STEME

:: MORE INFORMATION

Citation

STEME: a robust, accurate motif finder for large data sets.
Reid JE, Wernisch L.
PLoS One. 2014 Mar 13;9(3):e90735. doi: 10.1371/journal.pone.0090735. eCollection 2014.

MOCCS 1.6 – Motif Centrality Analysis of ChIP-Seq

MOCCS 1.6

:: DESCRIPTION

MOCCS is a method for for clarifying DNA-binding motif ambiguity.

::DEVELOPER

Haruka Ozaki, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • Perl

:: DOWNLOAD

 MOCCS

:: MORE INFORMATION

Citation

MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.
Ozaki H, Iwasaki W.
Comput Biol Chem. 2016 Feb 13. pii: S1476-9271(16)30030-5. doi: 10.1016/j.compbiolchem.2016.01.014.

Alien_hunter 1.7 – Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA

Alien_hunter 1.7

:: DESCRIPTION

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs).

::DEVELOPER

Georgios S. Vernikos and Julian Parkhill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Alien_hunter

:: MORE INFORMATION

Citation

Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
Vernikos GS and Parkhill J
Bioinformatics (Oxford, England)2006;22;18;2196-203

jEcho 1.0 – An Evolved Weight Vector to CHaracterize the protein’s post-translational Modification mOtifs

jEcho 1.0

:: DESCRIPTION

jEcho is an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.

::DEVELOPER

Fengfeng Zhou

:: SCREENSHOTS

jEcho

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Java

:: DOWNLOAD

 jEcho

:: MORE INFORMATION

Citation

Interdiscip Sci. 2015 Jun;7(2):194-9. doi: 10.1007/s12539-015-0260-2. Epub 2015 Aug 6.
jEcho: an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.
Zhao M, Zhang Z, Mai G, Luo Y, Zhou F.

ProtOn 2.3 – Description of Protein 3D structure in terms of Architecture, Topology and Motifs

ProtOn 2.3

:: DESCRIPTION

ProtOn (Proteins Online): 1) draws β-sheet maps, 2) detects architectures of all-β and α/β-classes and 3) detects structural motifs containing β-strands

::DEVELOPER

Evgeniy Aksianov (evaksianov@gmail.com)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

  ProtOn

:: MORE INFORMATION