:: DESCRIPTION
ProSMoS searches for 3D patterns in protein structures, e.g. find all proteins with a fold defined by a user.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
S-Y.Shi, B.Chitturi, and N.V.Grishin (2009)
“ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.”
Nucl. Acids Res. (2009) doi: 10.1093/nar/gkp316 First published online: May 6, 2009
:: DESCRIPTION
RISOTTO, extracts (long) 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, Laurent Marsan and Marie-France Sagot,
RISOTTO: Fast extraction of motifs with mismatches
In J. R. Correa, A. Hevia and M. Kiwi, editors, Proceedings of the 7th Latin American Theoretical Informatics Symposium, volume 3887 of Lecture Notes in Computer Science, pages 757-768. Springer-Verlag, 2006.
:: DESCRIPTION
GRISOTTO, uncovers motifs using prior information from a set of co-regulated DNA sequences.
:DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Alexandra M. Carvalho and Arlindo L. Oliveira,
GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge,
Algorithms for Molecular Biology, 6:13, Apr 2011.
:: DESCRIPTION
Sequence Searcher is an easy-to-use Java tool for searching protein and DNA sequences for user specified sequence motifs. The Sequence Searcher can search multiple sequences in a single pass. The target sequences may be imported from your computer in FASTA format or you can manually paste the sequence(s) into a text window.
::DEVELOPER
Dr. Chris Upton, University of Victoria, Biochemistry and Microbiology
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
N/A
:: DESCRIPTION
Voting is a software package that discovers common patterns, motif, in a set of DNA sequences. Voting is efficient to solve the planted (l,d) motif problem which discover a hidden length-l string motif appear in each input DNA sequence with at most d Hamming distance. Our package guarantees discovering all motifs in a short time.
::DEVELOPER
Bioinformatics Research Group of Hong Kong University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Francis Y.L. Chin and Henry C.M. Leung.
Voting Algorithms for Discovering Long Motifs (2005)
In Proceedings of Asia-Pacific Bioinformatics Conference (APBC) pages 261 – 271
:: DESCRIPTION
Compo is a software for composite motif discovery using discrete models.
::DEVELOPER
Geir Kjetil Sandve (geirksa@ifi.uio.no), Bioinformatics & Gene Regulation
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
RNAmotifs allows you to predict a structural motif common to a set of RNA sequences. The resulting motifs includes information on both RNA sequence and structure. Motifs are described both graphically and by a data file containing information on the underlying probabilistic model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rabani et. al,
Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes,
Proc Natl Acad Sci U S A., September 2008
:: DESCRIPTION
FMM allows you to find motifs that are discriminatively enriched in a positive sequences set relative to a negative sequences set. The main novelty is that it can learn a “Feature Motif Model” (FMM) representation of the motif, capturing dependencies between different positions through di-nucleotide features (such as: “G at position 3 and T at position 9”). Mono-nucleotide features are also in use, thus the FMM formalism contains the PSSM one. FMMs are represented by a clear and intuitive logo, easily pointing out important di-nucleotide features. The height of a feature in the logo is linear to its expected occurrence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sharon & Lubliner et al.,
A Feature-Based Approach to Modeling Protein-DNA Interactions,
PLoS Comput Biol, 4(8) Aug. 2008
:: DESCRIPTION
MotifOrganizer is designed to cluster large sets of DNA sequence motifs to identify common patterns. Different motif widths are allowed. It uses a two-stage divide-conquer-combine strategy to achieve scalability and efficiency.
::DEVELOPER
Steve Qin @ the Center for Statistical Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
FoldMiner performs structural similarity searches and rapid, unsupervised structural motif discovery. Motifs are used to improve the sensitivity and specificity of the search.
::DEVELOPER
The Brutlag Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Jessica Shapiro and Douglas L. Brutlag (2004).
FoldMiner: Structural Motif Discovery Using an Improved Superposition Algorithm.
Protein Science 13(1) 278-294.
