Journal article

A new generalized growth threshold for dynamic SOM for comparing average mutual information and oligonucleotide frequency as a species signature

CKK Chan, S Halgamuge

International Journal of Bio-Science and Bio-Technology | Published : 2009

Abstract

The average mutual information (AMI) known from information theory has been reported as a strong genome signature in some literature and we have reported the use of oligonucleotide frequencies as a genome signature. In this work we improve the use of AMI as a training feature for Growing Self Organising Maps (GSOM). Although the range of k is considered as an important parameter in AMI, no standard range for k is proposed. Our first contribution is to introduce a new growth threshold (GT) for GSOM and use it to identify the best range of k for clustering prokaryotic sequence fragments of 10 kb. We then, compare the results using the best k range of AMI against our previously published result..

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University of Melbourne Researchers

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