Name
Title | ||
|---|---|---|
Optimized numerical mapping scheme for filter-based exon location in DNA using a quasi-Newton algorithm |
Abstract | ||
|---|---|---|
An optimized numerical mapping scheme for achieving improved location of exons in DNA sequences using digital filters is proposed. Characteristic numerical values for the four nucleotides, referred to as pseudo-EIIP values, are obtained using a training procedure where the location accuracy is maximized using a quasi-Newton algorithm based on the Broyden-Fletcher-Goldfarb-Shanno updating formula. A training set of 80 DNA sequences is chosen from the HMR195 database. The objective function for the optimization procedure is formulated using the so-called receiver operating characteristic (ROC) technique and the procedure is initialized using electron-ion interaction potential (EIIP) values. Unbiased testing of the optimized characteristic values is carried out using a set of DNA sequences that has no overlap with the training set. Simulation results show that the pseudo-EIIP values yield more accurate exon locations than those obtained using the actual EIIP values. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1109/ISCAS.2010.5537209 | Circuits and Systems |
Keywords | Field | DocType |
DNA,Newton method,band-pass filters,biomedical communication,genomics,notch filters,optimisation,Broyden-Fletcher-Goldfarb-Shanno updating formula,DNA sequences,HMR195 database,bandpass notch digital filters,called receiver operating characteristic technique,electron-ion interaction potential,filter-based exon location,location accuracy,optimized numerical mapping scheme,pseudo-EIIP values,quasi-Newton algorithm,BFGS updating formula,DNA,ROC plots,bandpass notch digital filters,electron-ion interaction potential,exons,period-3 property | Training set,Band-stop filter,Digital filter,Receiver operating characteristic,Band-pass filter,Computer science,Algorithm,Electronic engineering,Biomedical communication,Newton's method | Conference |
ISSN | ISBN | Citations |
0271-4302 | 978-1-4244-5309-2 | 1 |
PageRank | References | Authors |
0.36 | 2 | 3 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Parameswaran Ramachandran | 1 | 1 | 0.36 |
| Wu-Sheng Lu | 2 | 296 | 24.90 |
| A. Antoniou | 3 | 267 | 30.79 |