相关论文: Suffix Arrays for Spaced-SNP Databases

Linguistic typology aims to capture structural and semantic variation across the world's languages. A large-scale typology could provide excellent guidance for multilingual Natural Language Processing (NLP), particularly for languages that…

We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…

Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…

In database design, Composite Keys are used to uniquely identify records and prevent data duplication. However, they require more memory and storage space than single keys, and can make queries more CPU-intensive. Surrogate Keys are an…

A panel of large number of common Single Nucleotide Polymorphisms (SNPs) distributed across an entire porcine genome has been widely used to represent genetic variability of pig. With the advent of SNP-array technology, a genome-wide…

Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…

It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…

When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We…

The ~4-Mbp basic genome shared by 32 independent isolates of E. coli representing considerable population diversity has been approximated by whole-genome multiple-alignment and computational filtering designed to remove mobile elements and…

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…

Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…

Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…

Beyond identifying genetic variants, we introduce a set of Boolean relations that allows for a comprehensive classification of the relations for every pair of variants by taking all minimal alignments into account. We present an efficient…

This work presents a mathematical model that establishes an interesting connection between nucleotide frequencies in human single-stranded DNA and the famous Fibonacci's numbers. The model relies on two assumptions. First, Chargaff's second…

Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…

The aetiology of polygenic obesity is multifactorial, which indicates that life-style and environmental factors may influence multiples genes to aggravate this disorder. Several low-risk single nucleotide polymorphisms (SNPs) have been…

Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…

The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…

To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…

We introduce a simple approach to understanding the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. The pipeline involves training deep convolutional neural networks…