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- Title
Data-intensive analysis of HIV mutations.
- Authors
Cintho Ozahata, Mina; Cerdeira Sabino, Ester; Sobhie Diaz, Ricardo; M. Cesar-Jr, Roberto; Ferreira, João Eduardo
- Abstract
Background: In this study, clustering was performed using a bitmap representation of HIV reverse transcriptase and protease sequences, to produce an unsupervised classification of HIV sequences. The classification will aid our understanding of the interactions between mutations and drug resistance. 10,229 HIV genomic sequences from the protease and reverse transcriptase regions of the pol gene and antiretroviral resistant related mutations represented in an 82-dimensional binary vector space were analyzed. Results: A new cluster representation was proposed using an image inspired by microarray data, such that the rows in the image represented the protein sequences from the genotype data and the columns represented presence or absence of mutations in each protein position.The visualization of the clusters showed that some mutations frequently occur together and are probably related to an epistatic phenomenon. Conclusion: We described a methodology based on the application of a pattern recognition algorithm using binary data to suggest clusters of mutations that can easily be discriminated by cluster viewing schemes.
- Subjects
HIV; REVERSE transcriptase; PROTEOLYTIC enzymes; VIRAL mutation; VIRAL genomes; DRUG resistance; CLUSTER analysis (Statistics); VECTOR spaces
- Publication
BMC Bioinformatics, 2015, Vol 16, Issue 1, p1
- ISSN
1471-2105
- Publication type
Article
- DOI
10.1186/s12859-015-0452-0