相关论文: Suffix Arrays for Spaced-SNP Databases

Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data…

Splicing sites provide unique statistics in human genome due to their large number and reasonably complete annotation. Analyses of the cumulative SNPs distribution in splicing sites reveal a few interesting observations. While a degree of…

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…

Single nucleotide polymorphisms (SNPs) often appear in clusters along the length of a chromosome. This is due to variation in local coalescent times caused by,for example, selection or recombination. Here we investigate whether…

As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaption that optimizes population survival in differing environments. This paper mathematically…

Biometric data is often highly sensitive, and a leak of this data can lead to serious privacy breaches. Some of the most sensitive of this type of data relates to the usage of DNA data on individuals. A leak of this type of data without…

Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…

Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv…

Various studies have shown an association between single nucleotide polymorphisms (SNPs) and common disease. We hypothesize that information encoded in the structure of SNP haploblock variation illumines molecular pathways and cellular…

Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…

After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…

Motivated by a non-random but clustered distribution of SNPs, we introduce a phenomenological model to account for the clustering properties of SNPs in the human genome. The phenomenological model is based on a preferential mutation to the…

The exploration of selected single nucleotide polymorphisms (SNPs) to identify genetic diversity between different sequencing population pools (Pool-seq) is a fundamental task in genetic research. As underlying sequence reads and their…

Single nucleotide polymorphisms (SNPs) represent an important type of dynamic sites within the human genome. These common variants often locally correlate into more complex multi-SNP haploblocks that are maintained throughout generations in…

In addition to variation in terms of single nucleotide polymorphisms (SNPs), whole regions ranging from several kilobases up to a megabase in length differ in copy number among individuals. These differences are referred to as Copy Number…

Capturing the vast amount of meaningful information encoded in the human genome is a fascinating research problem. The outcome of these researches have significant influences in a number of health related fields --- personalized medicine,…

We study the problem of indexing text with wildcard positions, motivated by the challenge of aligning sequencing data to large genomes that contain millions of single nucleotide polymorphisms (SNPs)---positions known to differ between…

The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…

Background: Structural Variations, SVs, in a genome can be linked to a disease or characteristic phenotype. The variations come in many types and it is a challenge, not only determining the variations accurately, but also conducting the…

Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…