title: Improved lower bounds of DNA tags based on a modified genetic algorithm.
abstract: The well-known massively parallel sequencing method is efficient and it can obtain sequence data from multiple individual samples. In order to ensure that sequencing, replication, and oligonucleotide synthesis errors do not result in tags (or barcodes) that are unrecoverable or confused, the tag sequences should be abundant and sufficiently different. Recently, many design methods have been proposed for correcting errors in data using error-correcting codes. The existing tag sets contain small tag sequences, so we used a modified genetic algorithm to improve the lower bound of the tag sets in this study. Compared with previous research, our algorithm is effective for designing sets of DNA tags. Moreover, the GC content determined by existing methods includes an imprecise range. Thus, we improved the GC content determination method to obtain tag sets that control the GC content in a more precise range. Finally, previous studies have only considered perfect self-complementarity. Thus, we considered the crossover between different tags and introduced an improved constraint into the design of tag sets.
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China.
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Wei
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Dong
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D001482:Base Composition; D020029:Base Pairing; D004247:DNA / Q000737:chemistry; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008957:Models, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA