Predicting nucleolar proteins using support-vector machines

Bodén, Mikael (2007). Predicting nucleolar proteins using support-vector machines. In: Alvis Brazma, Satoru Miyano and Tatsuya Akutsu, Proceedings of the 6th Asia-Pacific Bioinformatics Conference. 6th Asia-Pacific Bioinformatics Conference, Kyoto, Japan, (19-28). 14-17 January, 2008. doi:10.1142/9781848161092_0005

Author Bodén, Mikael
Title of paper Predicting nucleolar proteins using support-vector machines
Conference name 6th Asia-Pacific Bioinformatics Conference
Conference location Kyoto, Japan
Conference dates 14-17 January, 2008
Proceedings title Proceedings of the 6th Asia-Pacific Bioinformatics Conference
Journal name Series on Advances in Bioinformatics and Computational Biology
Place of Publication London, U.K.
Publisher Imperial College Press
Publication Year 2007
Sub-type Fully published paper
DOI 10.1142/9781848161092_0005
ISBN 9781848161085
ISSN 1751-6404
Editor Alvis Brazma
Satoru Miyano
Tatsuya Akutsu
Volume 6
Start page 19
End page 28
Total pages 10
Language eng
Formatted Abstract/Summary
The intra-nuclear organisation of proteins is based on possibly transient interactions with morphologically defined compartments like the nucleolus. The fluidity of trafficking challenges the development of models that accurately identify compartment membership for novel proteins. A growing inventory of nucleolar proteins is here used to train a support-vector machine to recognise sequence features that allow the automatic assignment of compartment membership. We explore a range of sequence-kernels and find that while some success is achieved with a profile-based local alignment kernel, the problem is ill-suited to a standard compartment-classification approach.
Subjects 0601 Biochemistry and Cell Biology
Keyword Nucleolus
Support-vector machine
Intra-nuclear protein localisation
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status UQ

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Created: Fri, 22 Jan 2010, 14:14:28 EST by Tara Johnson on behalf of Institute for Molecular Bioscience