Details

Autor(en) / Beteiligte

• Ramachandran, P
• Wu-Sheng Lu
• Antoniou, A

Titel

Optimized numerical mapping scheme for filter-based exon location in DNA using a quasi-Newton algorithm

Ist Teil von

• 2010 IEEE International Symposium on Circuits and Systems (ISCAS), 2010, p.2231-2234

Ort / Verlag

IEEE

Erscheinungsjahr

2010

Quelle

IEEE Electronic Library (IEL)

Beschreibungen/Notizen

• 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.