Neural networks for molecular sequence classification

Cathy Wu, Sailaja Shivakumar, Hsu-Ping Lin, Srinivas Veldurti and Yugesh Bhatikar

Mathematics and Computers in Simulation (MATCOM), 1995, vol. 40, issue 1, 23-33

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.

Keywords: Artificial neural network; Back propagation; Singular value decomposition; Molecular sequence analysis; Protein classification; Ribosomal RNA classification (search for similar items in EconPapers)
Date: 1995
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/0378475495000164
Full text for ScienceDirect subscribers only

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:matcom:v:40:y:1995:i:1:p:23-33

DOI: 10.1016/0378-4754(95)00016-4

Access Statistics for this article

Mathematics and Computers in Simulation (MATCOM) is currently edited by Robert Beauwens

More articles in Mathematics and Computers in Simulation (MATCOM) from Elsevier
Bibliographic data for series maintained by Catherine Liu ().