相关论文: Matching reads to many genomes with the $r$-index

This paper presents the R package gRapHD for efficient selection of high-dimensional undirected graphical models. The package provides tools for selecting trees, forests and decomposable models minimizing information criteria such as AIC or…

In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…

Software developers frequently reuse source code from repositories as it saves development time and effort. Code clones accumulated in these repositories hence represent often repeated functionalities and are candidates for reuse in an…

Data management on GPUs has become increasingly relevant due to a tremendous rise in processing power and available GPU memory. Similar to main-memory systems, there is a need for performant GPU-resident index structures to speed up query…

Providing architectural support is crucial for newly arising applications to achieve high performance and high system efficiency. Currently there is a trend in designing accelerators for special applications, while arguably a debate is…

To facilitate the review, evaluation and analysis of scientific literature, the lit-tag R Shiny application provides a convenient interface for users to generate a citation database with custom, user-defined tags and notes. Lit-tag is not…

Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…

Dense retrieval systems increasingly need to handle complex queries. In many realistic settings, users express intent through long instructions or task-specific descriptions, while target documents remain relatively simple and static. This…

We introduce the C++ application and R package ranger. The software is a fast implementation of random forests for high dimensional data. Ensembles of classification, regression and survival trees are supported. We describe the…

RNA secondary structures prediction is one of the main issues in bioinformatics. It seeks to elucidate structural conserved regions within a set of RNA sequences. Unfortunately, finding an accurate conserved structure is a very hard task to…

Finding desired information from large data set is a difficult problem. Information retrieval is concerned with the structure, analysis, organization, storage, searching, and retrieval of information. Index is the main constituent of an IR…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…

Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…

Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution…

We introduce the software tool NTRFinder to find the complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that nested…

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…

Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is an assay for DNA-protein-binding or post-translational chromatin/histone modifications. As with all high-throughput technologies, it requires a thorough…

Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…

FM-index is an efficient data structure for string search and is widely used in next-generation sequencing (NGS) applications such as sequence alignment and de novo assembly. Recently, FM-indexing is even performed down to the read level,…

Summary: R and Matlab are two high-level scientific programming languages which are frequently applied in computational biology. To extend the wide variety of available and approved implementations, we present the Rcall interface which runs…