Related papers: Detecting Mutations by eBWT
We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing…
The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression. It has become a fundamental tool for designing self-indexing data structures, with important applications in several area in science and…
It is known that the exact form of the Burrows-Wheeler-Transform (BWT) of a string collection depends, in most implementations, on the input order of the strings in the collection. Reordering strings of an input collection affects the…
In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…
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…
Motivation: Genome-Wide Association Studies (GWAS) seek to identify causal genomic variants associated with rare human diseases. The classical statistical approach for detecting these variants is based on univariate hypothesis testing, with…
Combining data from several case-control genome-wide association (GWA) studies can yield greater efficiency for detecting associations of disease with single nucleotide polymorphisms (SNPs) than separate analyses of the component studies.…
There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…
The Burrows-Wheeler Transform (BWT) is an invertible text transformation that permutes symbols of a text according to the lexicographical order of its suffixes. BWT is the main component of popular lossless compression programs (such as…
Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…
The Burrows-Wheeler Transform (BWT) is often taught in undergraduate courses on algorithmic bioinformatics, because it underlies the FM-index and thus important tools such as Bowtie and BWA. Its admirers consider the BWT a thing of beauty…
One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset…
A computationally simple genome-wide association study (GWAS) algorithm for estimating the main and epistatic effects of markers or single nucleotide polymorphisms (SNPs) is proposed. It is based on the intuitive assumption that changes of…
The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
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…
When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…
We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…
We present a new semi-external algorithm that builds the Burrows--Wheeler transform variant of Bauer et al. (a.k.a., BCR BWT) in linear expected time. Our method uses compression techniques to reduce computational costs when the input is…
The Burrows-Wheeler transform (BWT) is a permutation whose applications are prevalent in data compression and text indexing. The bijective BWT (BBWT) is a bijective variant of it. Although it is known that the BWT can be constructed in…