Neural networks for molecular sequence classification.

@article{citeulike:2771724, abstract = {A neural network classification method has been developed as an alternative approach to the search/organization problem of large molecular databases. Two artificial neural systems have been implemented on a Cray supercomputer for rapid protein/nucleic acid sequence classifications. The neural networks used are three-layered, feed-forward networks that employ back-propagation learning algorithm. The molecular sequences are encoded into neural input vectors by applying an n-gram hashing method or a SVD (singular value decomposition) method. Once trained with known sequences in the molecular databases, the neural system becomes an associative memory capable of classifying unknown sequences based on the class information embedded in its neural interconnections. The protein system, which classifies proteins into PIR (Protein Identification Resource) superfamilies, showed a 82\% to a close to 100\% sensitivity at a speed that is about an order of magnitude faster than other search methods. The pilot nucleic acid system, which classifies ribosomal RNA sequences according to phylogenetic groups, has achieved a 100\% classification accuracy. The system could be used to reduce the database search time and help organize the molecular sequence databases. The tool is generally applicable to any databases that are organized according to family relationships.}, address = {Department of Epidemiology/Biomathematics, University of Texas Health Center at Tyler 75710, USA.}, author = {Wu, C. and Berry, M. and Fung, Y. S. and McLarty, J. }, citeulike-article-id = {2771724}, issn = {1553-0833}, journal = {Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology}, keywords = {classification, molecular, neural\_networks, sequence}, pages = {429--437}, posted-at = {2008-05-08 15:04:58}, priority = {2}, title = {Neural networks for molecular sequence classification.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/7584367}, volume = {1}, year = {1993} }

TY - JOUR ID - citeulike:2771724 L3 - citeulike-article-id:2771724 TI - Neural networks for molecular sequence classification. JF - Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology VL - 1 SP - 429 EP - 437 AD - Department of Epidemiology/Biomathematics, University of Texas Health Center at Tyler 75710, USA. SN - 1553-0833 N2 - A neural network classification method has been developed as an alternative approach to the search/organization problem of large molecular databases. Two artificial neural systems have been implemented on a Cray supercomputer for rapid protein/nucleic acid sequence classifications. The neural networks used are three-layered, feed-forward networks that employ back-propagation learning algorithm. The molecular sequences are encoded into neural input vectors by applying an n-gram hashing method or a SVD (singular value decomposition) method. Once trained with known sequences in the molecular databases, the neural system becomes an associative memory capable of classifying unknown sequences based on the class information embedded in its neural interconnections. The protein system, which classifies proteins into PIR (Protein Identification Resource) superfamilies, showed a 82% to a close to 100% sensitivity at a speed that is about an order of magnitude faster than other search methods. The pilot nucleic acid system, which classifies ribosomal RNA sequences according to phylogenetic groups, has achieved a 100% classification accuracy. The system could be used to reduce the database search time and help organize the molecular sequence databases. The tool is generally applicable to any databases that are organized according to family relationships. KW - classification KW - molecular KW - neural_networks KW - sequence AU - Wu, C AU - Berry, M AU - Fung, YS AU - McLarty, J PY - 1993/// UR - http://view.ncbi.nlm.nih.gov/pubmed/7584367 ER -