Title | ||
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Iterative Refinement of Repeat Sequence Specification Using Constrained Pattern Matching |
Abstract | ||
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Repeated sequences in genome are structures which indicate important biological functions such as protein binding. They are associated with various genetic diseases. We consider the problem of finding a specification for a "significant" repeating pattern in a given sequence. A significant pattern carries high amount of information, and it has many non-overlapping repeats. We propose for this problem, a method that takes as input an initial specification for a repeating pattern. A pattern is specified by a sequence of letters separated by varying length wildcards. The method presents to the user maximal occurrences for the current pattern specification in a way that no text symbol can be shared as a letter by two different pattern occurrences. This reduces the begin-end position-overlaps among different occurrences. The user modifies the specification manually to eliminate overlapping repeats. This process continues until a specification for a significant pattern is obtained. |
Year | DOI | Venue |
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2007 | 10.1109/BIBE.2007.4375715 | BIBE |
Keywords | Field | DocType |
begin-end position-overlaps,vertex-disjoints path,pattern matching with wildcards,cellular biophysics,diseases,genetics,repeating pattern,iterative refinement,proteins,maximum flow,biological techniques,nonoverlapping repeats,molecular biophysics,edge disjoint path,genome,repeat sequence specification,repeats,protein binding,constrained pattern matching,genetic diseases,current pattern specification,pattern matching | Iterative refinement,Cellular biophysics,Wildcard character,Computer science,Algorithm,Maximum flow problem,Bioinformatics,Pattern matching | Conference |
ISBN | Citations | PageRank |
978-1-4244-1509-0 | 2 | 0.38 |
References | Authors | |
4 | 4 |
Name | Order | Citations | PageRank |
---|---|---|---|
Dan He | 1 | 14 | 0.88 |
Abdullah N. Arslan | 2 | 194 | 19.71 |
Yu He | 3 | 2 | 0.38 |
Xindong Wu | 4 | 8830 | 503.63 |