Pattern discovery

Wang, H.Y., Azuaje, F., and Black, N., Interactive GSOM-based approaches for improving biomedical pattern discovery and visualization, Proceedings Computer and Information Science, Lecture Notes in Computer Science (LNCS), Springer, Berlin, 3314, 556, 2004. 

Jason T. L. Wang, Bruce A. Shapiro, and Dennis Shasha, Pattern Discovery in Biomolecular Data Tools, Techniques and Applications, Oxford University Press, New York, 1999. 

The analysis was divided into two phases a pattern-discovery phase and a pattern-matching phase, as shown in Figure 4.7. In the pattern-discovery phase, a set of mass spectra of serum from both healthy and ovarian cancer-affected individuals were analyzed to identify a subset of key frequency values and their related amplitudes that are able to completely segregate the data... 

Rigoutscos, I., Floratos, A. (1998) Combinatorial pattern discovery in biological sequences The TEIRESIAS algorithm, Bioinformatics 14 55-67. 

Key Words Transcriptional regulation pattern discovery pattern matching phylogenetic footprinting prokaryotes RSAT get-orthologs retrieve-seq dyad-analysis. 

Below the link to the sequence, a list of buttons allows the user to send the retrieved sequences as input to a variety of pattern matching and pattern discovery tools. We will send the results to dyad-analysis. ... 

In prokaryotes, most transcription factors belong to the Helix-Turn-Helix family (19). Proteins of this class typically form homodimers, whose tridimensional structure is symmetrical. As a consequence, many prokaryote transcription factors bind to spaced motifs (also called dyads), where each halfmotif is bound by one element of the homodimer. The width of the spacing between the two contact points is transcription factor-specific, and can vary from 0 to 20 nt. Because we are working with bacterial sequences, we will illustrate the pattern discovery step by using a tool dedicated to the detection of spaced motifs dyad-analysis (20) (see Note 9). 

Choice of the pattern discovery algorithm. The program consensus, developed by Jerry Hertz, also gives pretty good results with bacterial promoters. It is, thus, a good idea to test both approaches, and compare the results. 

Key Words Transcriptional regulation pattern discovery coexpressed genes. 

The typical analysis, which is described in this protocol, consists in using successively different tools to go from a list of genes to a graphical map showing the instances of the significant motifs (sequence retrieval -> pattern discovery -> pattern matching -> feature-map). For this purpose, the tools are interconnected the result of one tool can be sent as input for the next tool (piping). 

This pattern discovery program oligo-analysis (1) detects significantly overrepresented oligonucleotides in a set of input sequences. We will use it to... 

Upstream region size. The efficiency of pattern discovery programs depends on the selected size. Default values have been determined in an organism-specific way (400 bp for bacteria, 800 bp for yeast,...). 

Sandelin, A., and Wasserman, W. W. (2004) Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol. 338, 207-215. 

Pattern discovery Associations/correlations Predictive ADME/Tox Population studies... 

Pattern discovery. The pattern such as (A, B, C,. ..) exists more than a specified number of times but does not of itself, in rawest form, state whether this is more, less, or as much as expected on the chance basis of A,B,C, and so on, coming together. It can discover very complex associations but not associations that ought to occur but don t. 

Noren GN, Bei vaU T, Ryan PB, Juhlin K, Schuemie MJ, Madigan D. 2013. Empirical performance of the calibrated self-controlled cohort analysis within temporal pattern discovery Lessons for developing a risk identification and analysis system. Drug Saf 36(Suppl. 1) S107-S121. doi 10.1007/s40264-013-0095-x. 

Noren G, Hopstadius J, Bate A, Star K, and Edwards I. 2010. Temporal pattern discovery in longitudinal electronic patient records. Data Mining and Knowledge Discover 20(3) 361-387. 

Fogel, G.F. (2008). Gomputational intelligence approaches for pattern discovery in biological systems. Briefings in Bioinformatics, Vol. 9, pp. 307-316. 

Mobasher, B., Jain, E., Han, E., and Srivastava, J. (19%). Web mining Pattern discovery from World Wide Web Transactions. Technical Report TR 96-050. 

The power of these methods lies in their ability to discern relationships in data that are inherently noisy. The data are treated as categorical rather that continuous active (yes), inactive (no) and a variable category of unassigned data (maybe). These methods are deterministic and, as such, derive all relationships between all compounds at all levels of support. The relationships or patterns are scored based on their information content. Unlike methods such as recursive partitioning, pattern discovery is not greedy and is complete. The discrimination ability of pattern discovery depends very much on the quality of the data generated and on the type and condition of the compounds if either is questionable, the... 

These approaches have been encoded into a family of algorithms known as pattern discovery (PD). 4 PD describes a family of novel methods in the category of data mining. One of the distinguishing features of PD is that it discovers rela-... 

PDB PDE PB PD PETSc PNNL PSC PUNCH Protein Data Bank partial differential eqnations Poisson-Boltzmann pattern discovery Portable, Extensible Toolkit for Scientific Compnting Pacific Northwest National Laboratory Pittsbnrgh Snpercompnting Center Pnrdne University Network Compnting Hnbs... 

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