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Abstract:

Motivation: There is a significant ongoing research to identify the number and types of repetitive DNA sequences. As more genomes are sequenced, efficiency and scalability in computational tools become mandatory. Existing tools fail to find distant repeats because they cannot accommodate whole chromosomes, but segments. Also, a quantitative framework for repetitive elements inside a genome or across genomes is still missing. Results: We present a new efficient algorithm and its implementation as a software tool to compute all perfect repeats in inputs of up to 500 million nucleotide bases, possibly containing many genomes. Our algorithm is based on a suffix array construction and a novel procedure to extract all perfect repeats in the entire input, that can be arbitrarily distant, and with no bound on the repeat length. We tested the software on the Homo sapiens DNA genome NCBI 36.49. We computed all perfect repeats of at least 40 bases occurring in any two chromosomes with exact matching. We found that each H. sapiens chromosome shares ∼10% of its full sequence with every other human chromosome, distributed more or less evenly among the chromosome surfaces. We give statistics including a quantification of repeats by diversity, length and number of occurrences. We compared the computed repeats against all biological repeats currently obtainable from Ensembl enlarged with the output of the dust program and all elements identified by TRF and RepeatMasker (ftp://ftp.ebi.ac.uk/pub/databases/ensembl/ jherrero/.repeats/all_repeats.txt.bz2). We report novel repeats as well as new occurrences of repeats matching with known biological elements. © The Author 2009. Published by Oxford University Press. All rights reserved.

Registro:

Documento: Artículo
Título:Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome
Autor:Becher, V.; Deymonnaz, A.; Heiber, P.
Filiación:Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
Palabras clave:article; bioinformatics; computer program; controlled study; gene sequence; genetic algorithm; human; human chromosome; human genome; intermethod comparison; nucleotide repeat; priority journal; Algorithms; Genome, Human; Genomics; Humans; Repetitive Sequences, Nucleic Acid; Homo sapiens
Año:2009
Volumen:25
Número:14
Página de inicio:1746
Página de fin:1753
DOI: http://dx.doi.org/10.1093/bioinformatics/btp321
Título revista:Bioinformatics
Título revista abreviado:Bioinformatics
ISSN:13674803
CODEN:BOINF
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v25_n14_p1746_Becher

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Citas:

---------- APA ----------
Becher, V., Deymonnaz, A. & Heiber, P. (2009) . Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome. Bioinformatics, 25(14), 1746-1753.
http://dx.doi.org/10.1093/bioinformatics/btp321
---------- CHICAGO ----------
Becher, V., Deymonnaz, A., Heiber, P. "Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome" . Bioinformatics 25, no. 14 (2009) : 1746-1753.
http://dx.doi.org/10.1093/bioinformatics/btp321
---------- MLA ----------
Becher, V., Deymonnaz, A., Heiber, P. "Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome" . Bioinformatics, vol. 25, no. 14, 2009, pp. 1746-1753.
http://dx.doi.org/10.1093/bioinformatics/btp321
---------- VANCOUVER ----------
Becher, V., Deymonnaz, A., Heiber, P. Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome. Bioinformatics. 2009;25(14):1746-1753.
http://dx.doi.org/10.1093/bioinformatics/btp321