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High performance computing of oligopeptides complete backtranslation applied to DNA microarray probe design
Author(s) -
Jaziri Faouzi,
Peyretaillade Eric,
Peyret Pierre,
Hill David R.C.
Publication year - 2016
Publication title -
concurrency and computation: practice and experience
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.309
H-Index - 67
eISSN - 1532-0634
pISSN - 1532-0626
DOI - 10.1002/cpe.3412
Subject(s) - computer science , dna microarray , software , oligonucleotide , speedup , parallel computing , dna , biology , programming language , gene , biochemistry , gene expression , genetics
Summary Complete backtranslation is the step of generating all possible nucleic acid sequences from a protein sequence. This is a time‐consuming task that can provide unreasonable quantities of data. Complete backtranslation was recently used to initiate probe design for functional DNA microarrays from conserved peptidic regions, in order to assess the full microbial gene diversity present in complex environments. In this article, we present an efficient parallelization method to compute a complete backtranslation of short peptides to select probes for functional microarrays. We implemented a software that uses meta‐programming and a model‐driven engineering approach to automatically generate source codes to perform complete backtranslation on different architectures: PCs, Symmetric Multiprocessors servers, computing clusters, or a computing grid. Our software is filtering the generated oligonucleotides with usual selection criteria for the design of microarray probes. It uses load balancing and can be easily integrated in probe design software for functional microarrays. We present its performance on both simulated and real biological datasets. The obtained results show a significant computing speedup on different platforms and an important gain of about 40% of disk space when filtering oligonucleotides. Copyright © 2014 John Wiley & Sons, Ltd.