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BiPad: de novo Discovery of Two-block Structured Motifs
The Children's Mercy Hospital
posted on 04/04/2011
Researchers at Children’s Mercy Hospital have devised a robust, efficient algorithm to search specified DNA regions for two-block structured motifs and have implemented it in computer software.
Suggested Uses
- Discover two-part regulatory motifs within DNA regions of interest
- Also finds more general two-block motifs, e.g. governing chromosomal matrix attachment or alternative transcriptions into protein isoforms
- Can be used to find one-block motifs of any user-speciifed length
Advantages
- Discovers motifs structured as two separated elements, rather than a single contiguous sequence as with most discovery methods
- Works with a variable and unknown gap between two elements of bipartite motifs
- Works with structured motifs and gaps of arbitrary length, and with any of the four possible orientations of the two parts
- Introductory use available at http://bipad.cmh.edu/
Detailed Description
Background
Completion of the human genome project opened the full genome to searches for both transcribed and regulatory regions.
One common type of regulatory region that occurs on the same chromosome as its corresponding gene consists of two sequences of 5-12 bases (bp) each, separated by a gap of several bp. This two-block, or bipartite, structured motif provides more regulatory flexibility than a single region, so is of special significance and interest to researchers.
Algorithms to search for single regulatory sequences in a given region of DNA usually maximize some information theoretic metric as a function of candidate sequence length and position.
Methods to search for two-block structured motifs are much more than twice as complex because maximization is also required over the unknown gap size between the two constituent blocks, and over the four possible orientations of the two parts.
The Innovation
Researchers at Children’s Mercy Hospital have devised a robust, efficient algorithm to search specified DNA regions for two-block structured motifs and have implemented it in computer software.
BiPad seeks to find a two-block structured motif (two sequence lengths, two positions, and gap size) with the highest information content (lowest entropy). It is “greedy” (deterministic) in the sense that it takes advantage of all the information available at each step of the optimization.
BiPad is written in C++ for the GNU compiler with the Standard Template Library on Linux , Unix, or Mac OS X systems.
Applications
- Discover two-part regulatory motifs within DNA regions of interest
- Also finds more general two-block motifs, e.g. governing chromosomal matrix attachment or alternative transcriptions into protein isoforms
- Can be used to find one-block motifs of any user-speciifed length
Advantages
- Discovers motifs structured as two separated elements, rather than a single contiguous sequence as with most discovery methods
- Works with a variable and unknown gap between two elements of bipartite motifs
- Works with structured motifs and gaps of arbitrary length, and with any of the four possible orientations of the two parts
- Introductory use available at http://bipad.cmh.edu/
Status
Limitations
Available only to non-profit organizations for research purposes.
File Number: 2011-006
Web site: http://bipad.cmh.edu/
| Copyright: | Children’s Mercy Hospital |
|---|---|
| Trademark: | Yes |
This innovation currently is not available for online licensing. Please contact Stephen ONeil at The Children's Mercy Hospital for more information.
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