- author = "W. B. Langdon",
- title = "Performance of Genetic Programming Optimised {Bowtie2} on Genome Comparison and Analytic Testing ({GCAT}) Benchmarks",
- journal = "BioData Mining",
- year = "2015",
- volume = "8",
- number = "1",
- month = "8 " # jan,
-
keywords = "genetic algorithms, genetic programming, genetic
improvement, GI, double-ended DNA sequence, high
throughput Solexa 454 nextgen NGS sequence
query,
Bowtie2GP, rapid fuzzy string matching, Homo sapiens genome reference consortium HG19
Next-generation DNA sequencing,
",
-
URL = "
http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/papers/Langdon_2014_BDM.pdf",
-
DOI = "
doi:10.1186/s13040-014-0034-0",
- size = "8 pages",
-
abstract = "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:
Bowtie2GP and the original Bowtie2 release were compared on bioplanet's GCAT synthetic benchmarks. Bowtie2GP 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 45percent faster than Bowtie2. The lost in accuracy can be as little as 0.2--0.5percent but up to 2.5percent for longer sequences.",
-
notes = "GISMO
PMID: 25621011 [PubMed]",
