Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 10 of 10 for “"Motif Finding"”.
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Assessing effects of symmetry on motif finding
… and compare the ability of three methods of a motif-finding program, consensus, taking into account orientation to accurately predict variable symmetric/asymmetric true binding site models. The three consensus methods included the c0 method which ignores the complement of a sequence. In this …
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Statistical physics and biological information : hydrophobicity patterns in protein design and differential motif finding in DNA
… goal, the recognition and identification of DNA motifs--short patterns in biological sequences--is essential. Common examples of motifs include transcription factor binding sites in promoter regions of co-regulated genes and exonic and intronic splicing enhancers ...
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Extracting regulatory signals from DNA sequences using syntactic pattern discovery
… Coli, with known instances of regulatory motifs collected from biological literature, the algorithm showed, in 14 cases, a high sensitivity and specificity of 70% and 80%, respectively. TABS was shown to perform better than two other popular state-of-the-art motif-finding algorithms. In …
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MCAT: Motif Combining and Association Tool
De novo motif discovery in biological sequences is an important and computationally challenging problem. A myriad of algorithms have been developed to solve this problem with varying success, but it can be difficult for even a small number of these tools to reach a consensus. Because individual …
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A Biclustering Approach to Combinatorial Transcription Control
… the transcription factors bind. Conventional motif finding algorithms fail to address this issue. We propose a novel biclustering algorithm based on random sampling to identify candidate binding site combinations. We establish bounds on the various parameters to the algorithm and study the …
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Novel Sequence-Based Method for Identifying Transcription Factor Binding Sites in Prokaryotic Genomes
… DNA as homodimers, leading to their palindromic motif specificities. The connection between the TF and its promoter is based on the autoregulation phenomenon noticed in E. coli. Approximately 55% of the TFs analyzed were estimated to be autoregulated. Our preliminary analysis using RegulonDB …
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In silico approaches to investigating mechanisms of gene regulation
… data, and advances in alignment algorithms and motif-finding methods, provide opportunities to tackle the important task of dissecting how genes are regulated. Genes exhibiting similar expression profiles are often regulated by common transcription factors. We developed a method for identifying …
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Finding Interesting Subgraphs with Guarantees
… as anomaly detection, dense subgraph mining, motif finding, information diffusion, and epidemic spread. A common underlying task in all these problems is finding an "interesting subgraph"; that is, finding a part of the graph---usually small relative to the whole---that optimizes a score …
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Modeling And Identification Of Differentially Regulated Genes Using Transcriptomics And Proteomics Data
… DCMU treatment, combined with data mining and motif finding algorithms led to a discovery of novel transcription factor, RRTF1 that responds to redox stresses in <italic>Arabidopsis thaliana</italic>. Time course transcriptomics data from <italic>Cyanothece</italic> sp. ATCC 51142 have shown …
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Protein-DNA Binding: Discovering Motifs and Distinguishing Direct from Indirect Interactions
… and replication, the specific DNA binding motifs of many regulatory proteins and complexes are still to be determined. For this purpose, many computational tools for DNA motif discovery have been developed in the last two decades. These tools employ a variety of strategies, from exhaustive …