Related papers: Indexing large genome collections on a PC

C++ code snippets from a multi-core parallel memory-efficient crossover for genetic programming are given. They may be adapted for separate generation evolutionary algorithms where large chromosomes or small RAM require no more than M + (2…

Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. It is used to identify the co-expressed genes in specific cells or tissues that are actively…

Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise.…

Similarity search, the task of identifying objects most similar to a given query object under a specific metric, has gathered significant attention due to its practical applications. However, the absence of coordinate information to…

Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…

Motivation: Microarray data has been recently been shown to be efficacious in distinguishing closely related cell types that often appear in the diagnosis of cancer. It is useful to determine the minimum number of genes needed to do such a…

One of the most popular tools for large scale gene expression studies are high-density oligonucleotide (GeneChip(R)) arrays. These currently have 16-20 small probe cells (``features'') for evaluating the transcript abundance of each gene.…

The problem of fast items retrieval from a fixed collection is often encountered in most computer science areas, from operating system components to databases and user interfaces. We present an approach based on hash tables that focuses on…

Similarity search approaches based on graph walks have recently attained outstanding speed-accuracy trade-offs, taking aside the memory requirements. In this paper, we revisit these approaches by considering, additionally, the memory…

In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably…

This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…

Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…

Metagenomics is an emerging field of molecular biology concerned with analyzing the genomes of environmental samples comprising many different diverse organisms. Given the nature of metagenomic data, one usually has to sequence the genomic…

Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the…

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.

Given two unsorted lists each of length N that have a single common entry, a quantum computer can find that matching element with a work factor of $O(N^{3/4}\log N)$ (measured in quantum memory accesses and accesses to each list). The…

Developments in Genome-Wide Association Studies have led to the increasing notion that future healthcare techniques will be personalized to the patient, by relying on genetic tests to determine the risk of developing a disease. To this end,…

Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…

This paper develops a memory-efficient approach for Sequential Pattern Mining (SPM), a fundamental topic in knowledge discovery that faces a well-known memory bottleneck for large data sets. Our methodology involves a novel hybrid trie data…

Duplication, whether exact or partial, is a common issue in many datasets. In clinical notes data, duplication (and near duplication) can arise for many reasons, such as the pervasive use of templates, copy-pasting, or notes being generated…