Related papers: Seed design framework for mapping SOLiD reads

Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…

Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…

We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We…

This paper presents an accurate short-read mapper for next-generation sequencing data which is widely used in the 1000 Genomes Project, and human clinical and other species genome studies.

There is a growing interest in designing Graph Neural Networks (GNNs) for seeded graph matching, which aims to match two unlabeled graphs using only topological information and a small set of seed nodes. However, most previous GNNs for this…

Algorithms for machine learning-guided design, or design algorithms, use machine learning-based predictions to propose novel objects with desired property values. Given a new design task -- for example, to design novel proteins with high…

Matching local features across images is a fundamental problem in computer vision. Targeting towards high accuracy and efficiency, we propose Seeded Graph Matching Network, a graph neural network with sparse structure to reduce redundant…

Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…

In this paper, we propose a semi-supervised deep learning method for detecting the specific types of reads that impede the de novo genome assembly process. Instead of dealing directly with sequenced reads, we analyze their coverage graphs…

Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…

Photonic inverse design has emerged as an indispensable engineering tool for complex optical systems. In many instances it is important to optimize for both material and geometry configurations, which results in complex non-smooth search…

We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We…

Symbolic regression is the process of identifying mathematical expressions that fit observed output from a black-box process. It is a discrete optimization problem generally believed to be NP-hard. Prior approaches to solving the problem…

High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…

Manifold learning techniques have become increasingly valuable as data continues to grow in size. By discovering a lower-dimensional representation (embedding) of the structure of a dataset, manifold learning algorithms can substantially…

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…

Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…

Ongoing progress in computational intelligence (CI) has led to an increased desire to apply CI techniques for the purpose of improving software engineering processes, particularly software testing. Existing state-of-the-art automated…

Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…

We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt…