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Garcia-2011a

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Article

Title Minimal absent words in prokaryotic and eukaryotic genomes
Author Sara Pinto Garcia, Armando J. Pinho, João M. O. S. Rodrigues, Carlos A C Bastos, Paulo J S G Ferreira
Journal PLoS ONE
Volume 6
Number 1
Pages e16065
Month January
Year 2011
DOI 10.1371/journal.pone.0016065
Group
Group (before 2015) Signal Processing Laboratory, Transverse Activity on Innovative Biomedical Technologies
Indexed by ISI Yes

Abstract

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we explore different sets of minimal absent words in the genomes of 22 organisms (one archaeota, thirteen bacteria and eight eukaryotes). We investigate if the mutational biases that may explain the deficit of the shortest absent words in vertebrates are also pervasive in other absent words, namely in minimal absent words, as well as to other organisms. We find that the compositional biases observed for the shortest absent words in vertebrates are not uniform throughout different sets of minimal absent words. We further investigate the hypothesis of the inheritance of minimal absent words through common ancestry from the similarity in dinucleotide relative abundances of different sets of minimal absent words, and find that this inheritance may be exclusive to vertebrates.