Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

Background Genetic studies are increasingly based on short noisy next generation scanners. Typically complete DNA sequences are assembled by matching short NextGen sequences against reference genomes. Despite considerable algorithmic gains since the turn of the millennium, matching both single ended...

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Vydané v:BioData mining Ročník 8; číslo 1; s. 1
Hlavný autor: Langdon, W B
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 08.01.2015
BioMed Central Ltd
Predmet:
Algorithms
Benchmarks
Bioinformatics
Biomedical and Life Sciences
Comparative analysis
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Data Mining and Knowledge Discovery
Deoxyribonucleic acid
DNA sequencing
Gene sequencing
Genetic algorithms
Genomes
Genomics
Life Sciences
Matching
Methods
Nucleotide sequencing
Scanners
Short Report
Technology application
High throughput Solexa 454 nextgen NGS sequence query
Rapid fuzzy string matching
Double-ended DNA sequence
Homo sapiens genome reference consortium HG19
ISSN:1756-0381, 1756-0381
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Shrnutí:Background Genetic studies are increasingly based on short noisy next generation scanners. Typically complete DNA sequences are assembled by matching short NextGen sequences against reference genomes. Despite considerable algorithmic gains since the turn of the millennium, matching both single ended and paired end strings to a reference remains computationally demanding. Further tailoring Bioinformatics tools to each new task or scanner remains highly skilled and labour intensive. With this in mind, we recently demonstrated a genetic programming based automated technique which generated a version of the state-of-the-art alignment tool Bowtie2 which was considerably faster on short sequences produced by a scanner at the Broad Institute and released as part of The Thousand Genome Project. Results Bowtie2 G P and the original Bowtie2 release were compared on bioplanet’s GCAT synthetic benchmarks. Bowtie2 G P enhancements were also applied to the latest Bowtie2 release (2.2.3, 29 May 2014) and retained both the GP and the manually introduced improvements. Conclusions On both singled ended and paired-end synthetic next generation DNA sequence GCAT benchmarks Bowtie2GP runs up to 45% faster than Bowtie2. The lost in accuracy can be as little as 0.2–0.5% but up to 2.5% for longer sequences.
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content type line 23
ISSN:1756-0381
1756-0381
DOI:10.1186/s13040-014-0034-0