A comparison between hierarchical clustering and community detection method in the collection of gene targets for molecular identification of pathogenic fungi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Ribosomal RNA sequence is a popular primary molecular target in the diagnosis of many fungal and bacterial infections. More recently a number of other molecular targets like 'cytochrome b', 'rpoB', 'actin' is available in public databases such as GenBank. These sequences could be better alternatives to the popular ribosomal RNA as molecular targets. However, existing computational approaches do not provide a convenient method to collect and make these sequences available for the development of new alternative sequence-based diagnostics that are critical for early detection of infectious agents like fungi. The long-term goal of this study is to develop a computational tool for the rapid identification of infectious agents in biological sample. In the present study, we focus on pre-processing of sequence data in public database and compare a number of clustering approaches to classify currently available DNA sequences into different target genes. We evaluate the correctness of these methods based on the target classification of seven different species of Zygomycetes. Use of a clustering comparison metric has shown that community detection and hierarchical clustering methods are on par with high accuracy.

Original languageEnglish (US)
Title of host publicationProceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012
Pages756-761
Number of pages6
DOIs
StatePublished - Dec 1 2012
Event2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012 - Philadelphia, PA, United States
Duration: Oct 4 2012Oct 7 2012

Publication series

NameProceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012

Conference

Conference2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012
CountryUnited States
CityPhiladelphia, PA
Period10/4/1210/7/12

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Keywords

  • Clustering
  • Community Detection
  • Gene Targets
  • Sequence-based Molecular Identification
  • Zygomycetes

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Thapa, I., Bhowmick, S., & Bastola, D. R. (2012). A comparison between hierarchical clustering and community detection method in the collection of gene targets for molecular identification of pathogenic fungi. In Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012 (pp. 756-761). [6470234] (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012). https://doi.org/10.1109/BIBMW.2012.6470234