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

Chan, Chon-Kit Kenneth and Halgamuge, Saman (2009) A new generalized growth threshold for dynamic SOM for comparing average mutual information and oligonucleotide frequency as a species signature. International Journal of Bio-Science and Bio-Technology, 1 1: 1-10.

Author Chan, Chon-Kit Kenneth
Halgamuge, Saman
Title A new generalized growth threshold for dynamic SOM for comparing average mutual information and oligonucleotide frequency as a species signature
Journal name International Journal of Bio-Science and Bio-Technology   Check publisher's open access policy
Publication date 2009-12
Sub-type Article
Volume number 1
Issue number 1
ISSN 2233-7849
Start page 1
End page 10
Total pages 10
Place of publication Daedoek-Gu, Daejon, Korea, Republic of
Publisher Science and Engineering Research Support Society
Language eng
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 results using oligonucleotide frequencies. These experiments showed that the newly proposed GT equation makes GSOM able to efficiently and effectively analyse different data features for the same data. The results also emphasize our use of oligonucleotide frequencies as opposed to AMI.
Keyword GSOM
AMI
Species separation
Prokaryotic sequences
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article
Collection: School of Agriculture and Food Sciences
 
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Created: Tue, 22 Mar 2011, 22:48:51 EST by Dr Chon-Kit Kenneth Chan on behalf of School of Agriculture and Food Sciences