:: DESCRIPTION
The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: MORE INFORMATION
Citation
Schreiber, F. and Schwöbbermeyer H.
MAVisto: a tool for the exploration of network motifs.
Bioinformatics, 21, 3572-3574, 2005.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
UnderlyingFilter is a software of filtering degenerate motifs to protein sequence analysis
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
M. Comin, D. Verzotto,
“Filtering Degenerate Motifs with Application to Protein Sequence Analysis“,
Algorithms 6, no. 2: pp. 352-370.
:: DESCRIPTION
RISO is a software to extract conserved regions that occur in a well-ordered and regularly spaced manner in a set of DNA sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira and Marie-France Sagot,
An efficient algorithm for the identification of structured motifs in DNA promoter sequences,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(2):126-140, Apr-Jun, 2006.
:: DESCRIPTION
MUSA (Motif finding using an UnSupervised Approach) is a new algorithm that can be used either to autonomously find over-represented complex motifs or to estimate search parameters for modern motif finders.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mendes ND, Casimiro AC, Santos PM, Sá-Correia I, Oliveira AL, Freitas AT.
MUSA: a parameter free algorithm for the identification of biologically significant motifs.
Bioinformatics. 2006 Dec 15; 22(24): 2996-3002
:: DESCRIPTION
The LearnCoil Histidase Kinase program uses an iterative learning algorithm to detect possible coiled-coil domains in histidase kinase receptors.
The LearnCoil-VMF program uses an iterative learning algorithm to detect coiled-coil-like regions in viral membrane-fusion proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains.
Singh M, Berger B, Kim PS, Berger JM, Cochran AG.
Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):2738-43.
LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins.
Singh M, Berger B, Kim PS.
J Mol Biol. 1999 Jul 30;290(5):1031-41.
:: DESCRIPTION
MoTeX is an accurate and efficient tool for MoTif eXtraction.
:: DEVELOPER
Dr. Solon P. Pissis
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Solon P. Pissis, Alexandros Stamatakis, and Pavlos Pavlides.
MoTeX: a word-based HPC tool for MoTif eXtraction.
the Fourth ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2013), pp. 13-22, 2013. ACM Digital Library