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Issue No. 03 - May-June (2013 vol. 10)
ISSN: 1545-5963
pp: 793-798
Sara P. Garcia , University of Aveiro, Aveiro
Joao M. O. S. Rodrigues , University of Aveiro, Aveiro
Sergio Santos , University of Aveiro, Aveiro
Diogo Pratas , University of Aveiro, Aveiro
Vera Afreixo , University of Aveiro, Aveiro
Carlos Bastos , University of Aveiro, Aveiro
Paulo J. S. G. Ferreira , University of Aveiro, Aveiro
Armando J. Pinho , University of Aveiro, Aveiro
Genome assemblies are typically compared with respect to their contiguity, coverage, and accuracy. We propose a genome-wide, alignment-free genomic distance based on compressed maximal exact matches and suggest adding it to the benchmark of commonly used assembly quality metrics. Maximal exact matches are perfect repeats, without gaps or misspellings, which cannot be further extended to either their left- or right-end side without loss of similarity. The genomic distance here proposed is based on the normalized compression distance, an information-theoretic measure of the relative compressibility of two sequences estimated using multiple finite-context models. This measure exposes similarities between the sequences, as well as, the nesting structure underlying the assembly of larger maximal exact matches from smaller ones. We use four human genome assemblies for illustration and discuss the impact of genome sequencing and assembly in the final content of maximal exact matches and the genomic distance here proposed.
Bioinformatics, Genomics, Assembly, Sequential analysis, Computational biology, Materials

S. P. Garcia et al., "A Genomic Distance for Assembly Comparison Based on Compressed Maximal Exact Matches," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 3, pp. 793-798, 2013.
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