To allow for the presence of its varying forms, a protein motif is represented by a shorthand as follows: [XY] means "either X or Y" and {X} means "any amino acid except X." For example, the N-glycosylation motif is written as N{P}[ST]{P}. You can see the complete description...
Finding Genes by Hidden Markov Models with a Protein Motif DictionaryKiyoshi AsaiTetsushi YadaKatunobu Itou
(2006) A correlated motif approach for finding short linear motifs from protein interaction networks. BMC Bioinformatics, 7, 502.S.H. Tan, W. Hugo, W.K. Sung & S.K. Ng: A correlated motif approach for finding short linear motifs from protein interaction networks. BMC Bioinformatics 7, ...
DNA motifs are a set of specific binding sequences of a TF, characterized by a recurring pattern known as its motif pattern, which reflects the TF’s binding preferences and specificity [2]. Motif finding aims to find conserved transcription factors binding sites (TFBSs) from high-throughput ...
R. et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446, 806–810 (2007). Article CAS PubMed Google Scholar Rual, J. F. et al. Towards a proteome-scale map of the human protein-protein interaction network. ...
However, a footprinting fragment can contain no sequences similar to known protein recognition sites. Inspection of genome fragments nearby can help to identify missing site positions. RESULTS: Genome fragments containing footprints were supplied to a pipeline that constructed a position weight matrix (...
Identification of transcription factor binding sites (also called ‘motif discovery’) in DNA sequences is a basic step in understanding genetic regulation. Although many successful programs have been developed, the problem is far from being solved on ac
(2002-2006)GraduateResearchAssistanttoProf.Ming-YangKaoProjects:MotifFindinginBiosequencesABottleneckTravelingSalesmanProblemforNMRproteinstructurepredictionCombinatorialDNAWordDesignPolymorphicWormSignatureGenerationIndianInstituteofTechnologyDelhi(2001-2002)UndergraduateB.Tech.ResearchProjectAdvisorProf.SandeepSenThesis:...
a zinc finger protein PRDM9 was reported to regulate recombination hotspots in human and mouse genomes. In addition, a 13-mer motif contained in the binding sites of PRDM9 is found to be enriched in human hotspots. However, this 13-mer motif only covers a fraction of hotspots, indicating ...
The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in proteinbinding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if a clique consisting of a suffciently large number...