Results 261 to 270 of about 10,955,529 (276)

K-mer Mapping and RDBMS Indexes

2020
K-mer Mapping, an internal process for De Novo NGS genome fragments assembly methods, constitutes a computational challenge due to its high main memory consumption. We present a study of index-based methods to deal with this problem, considering a RDBMS environment.
Elvismary Molina de Armas, Paulo Cavalcanti Gomes Ferreira, Edward Hermann Haeusler, Maristela Terto de Holanda, Sérgio Lifschitz   +4 more
openaire   +1 more source

Fast detection of maximal exact matches via fixed sampling of query K-mers and Bloom filtering of index K-mers

Bioinform., 2019
MOTIVATION Detection of maximal exact matches (MEMs) between two long sequences is a fundamental problem in pairwise reference-query genome comparisons.
Yuansheng Liu, Leo Yu Zhang, Jinyan Li
semanticscholar   +1 more source

Efficient techniques for k-mer counting

2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2015
A large number of bioinformatics applications require counting of k-length substrings in genetically important long strings. K-mer counting generates the frequencies of each k-length substring in genome sequences. Genome assembly, repeat detection, multiple sequence alignment, error detection, and many other related applications use k-mer counting as a
Abdullah-Al Mamun, Soumitra Pal, Sanguthevar Rajasekaran   +2 more
openaire   +1 more source

Vectorizing the computation of k-mers

2018 13th Iberian Conference on Information Systems and Technologies (CISTI), 2018
In this article, a vectorization model of k-mers is presented and evaluated in order to enable its massive parallel processing on many core platforms. The model is made up of data structures and functions indexed in N-dimensional spaces that facilitate the massive parallelization of the main operations with k-mers. The model was implemented using a set
openaire   +1 more source

Classification of riboswitch sequences using k-mer frequencies

Biosystems, 2018
Riboswitches are non-coding RNAs that regulate gene expression by altering the structural conformation of mRNA transcripts. Their regulation mechanism might be exploited for interesting biomedical applications such as drug targets and biosensors. A major challenge consists in accurately identifying metabolite-binding RNA switches which are structurally
Hugo A. Guillén-Ramírez, Israel M. Martínez-Pérez   +1 more
openaire   +2 more sources

SubPhaser: A robust allopolyploid subgenome phasing method based on subgenome-specific k-mers.

New Phytologist, 2022
Kaihua Jia, Zhao-Xuan Wang, Long Wang, Guangjun Li, Wei Zhang, Xiao-Ling Wang, Fang-Ji Xu, Si-Qian Jiao, Shanshan Zhou, Hui Liu, Yongpeng Ma, Guiqi Bi, Wei Zhao, Y. El-Kassaby, I. Porth, Guowei Li, Ren-Gang Zhang, Jian-Feng Mao   +17 more
semanticscholar   +1 more source

Computational Performance Assessment of k-mer Counting Algorithms

Journal of Computational Biology, 2016
This article is about the assessment of several tools for k-mer counting, with the purpose to create a reference framework for bioinformatics researchers to identify computational requirements, parallelizing, advantages, disadvantages, and bottlenecks of each of the algorithms proposed in the tools.
Nelson, Pérez, Miguel, Gutierrez, Nelson, Vera   +2 more
openaire   +2 more sources

Compact Universal k-mer Hitting Sets

2016
We address the problem of finding a minimum-size set of k-mers that hits L-long sequences. The problem arises in the design of compact hash functions and other data structures for efficient handling of large sequencing datasets. We prove that the problem of hitting a given set of L-long sequences is NP-hard and give a heuristic solution that finds a ...
Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford   +4 more
openaire   +1 more source

Kmer-indexer: A Fast K-mer Indexing Program

2015
In our previous work, a k-mer based program named MFEprimer-2.0 was designed and developed for primer specificity evaluation task. In order to increase the index processing speed, decrease the index data size and memory usage, we developed a new program named kmer-indexer.
Wang, Xiaolei, Qu, Wubin, Zhang, Chenggang, Zhao, Dongsheng   +3 more
openaire   +2 more sources

Quill: A Memory Efficient k-mer Counting and k-mer Querying Tool for Commodity Clusters

2022 14th International Conference on Bioinformatics and Biomedical Technology, 2022
Budvin Edippuliarachchi, Damika Gamlath, Ruchin Amaratunga, Gunavaran Brihadiswaran, Sanath Jayasena   +4 more
openaire   +1 more source