Analyze influenza virus sequences using binary encoding approach

Ham Ching Lam, Daniel Boley

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

Abstract

Capturing mutation patterns of each individual influenza virus sequence is often challenging; in this paper, we demon- strated that using a binary encoding scheme coupled with dimension reduction technique, we were able to capture the intrinsic mutation pattern of the virus. Our approach looks at the variance between sequences instead of the commonly used p-distance or Hamming distance. We first convert the influenza genetic sequence to a binary string and then ap- ply Principal Component Analysis (PCA) to the converted sequence. PCA also provides a prediction capability for de- tecting reassortant virus by using data projection technique. Due to the sparsity of the binary string, we were able to analyze large volume of influenza sequence data in a very short time. For protein sequences, our scheme also allows the incorporation of biophysical properties of each amino acid. Here, we present various results from analyzing in- fluenza nucleotide, protein and genome sequences using the proposed approach. With the Next-Generation Sequencing (NGS) promises of sequencing DNA at unprecedented speed and production of massive quantity of data, it is imperative that new technique needs to be developed to provide quick and reliable analysis of any sequence data. Here, we believe our approach can be used at the upstream stage of sequence data analysis pipeline to gain insight as to which direction should be continued on in analyzing the available data.

Original languageEnglish (US)
Title of host publication10th International Workshop on Data Mining in Bioinformatics, BIOKDD 2011 - Held in Conjunction with SIGKDD Conference, the 17th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, KDD-2011
PublisherAssociation for Computing Machinery
Volume2011-August
ISBN (Electronic)9781450308397
ISBN (Print)9781450308397
DOIs
StatePublished - 2011
Event10th International Workshop on Data Mining in Bioinformatics, BIOKDD 2011 - San Diego, United States
Duration: Aug 21 2011Aug 21 2011

Publication series

NameProceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining

Other

Other10th International Workshop on Data Mining in Bioinformatics, BIOKDD 2011
CountryUnited States
CitySan Diego
Period8/21/118/21/11

Keywords

  • Binary encoding
  • Evolution
  • Influenza virus
  • Principal component analysis

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