A survey on data compression methods for biological sequences

M Hosseini, D Pratas, AJ Pinho - Information, 2016 - mdpi.com
The ever increasing growth of the production of high-throughput sequencing data poses a
serious challenge to the storage, processing and transmission of these data. As frequently …

GReEn: a tool for efficient compression of genome resequencing data

AJ Pinho, D Pratas, SP Garcia - Nucleic acids research, 2012 - academic.oup.com
Research in the genomic sciences is confronted with the volume of sequencing and
resequencing data increasing at a higher pace than that of data storage and communication …

Efficient DNA sequence compression with neural networks

M Silva, D Pratas, AJ Pinho - GigaScience, 2020 - academic.oup.com
Background The increasing production of genomic data has led to an intensified need for
models that can cope efficiently with the lossless compression of DNA sequences. Important …

GeCo2: An optimized tool for lossless compression and analysis of DNA sequences

D Pratas, M Hosseini, AJ Pinho - Practical Applications of Computational …, 2020 - Springer
The development of efficient DNA data compression tools is fundamental for reducing the
storage, given the increasing availability of DNA sequences. The importance is also …

An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

D Pratas, RM Silva, AJ Pinho, PJSG Ferreira - Scientific reports, 2015 - nature.com
Species evolution is indirectly registered in their genomic structure. The emergence and
advances in sequencing technology provided a way to access genome information, namely …

Design and development of bioinformatics feature based DNA sequence data compression algorithm

K Banerjee, V Bali - EAI Endorsed Transactions on Pervasive Health and …, 2019 - eudl.eu
INTRODUCTION: Genetic data plays a key role in the healthcare area in specific, but they
are typically very large in size. Many research shows that absence of DNA information at the …

Substitutional tolerant Markov models for relative compression of DNA sequences

D Pratas, M Hosseini, AJ Pinho - 11th International Conference on …, 2017 - Springer
Referential compression is one of the fundamental operations for storing and analyzing DNA
data. The models that incorporate relative compression, a special case of referential …

Metagenomic composition analysis of an ancient sequenced polar bear jawbone from Svalbard

D Pratas, M Hosseini, G Grilo, AJ Pinho, RM Silva… - Genes, 2018 - mdpi.com
The sequencing of ancient DNA samples provides a novel way to find, characterize, and
distinguish exogenous genomes of endogenous targets. After sequencing, computational …

DNA-COMPACT: DNA COM pression Based on a P attern-A ware C ontextual Modeling T echnique

P Li, S Wang, J Kim, H Xiong, L Ohno-Machado… - PloS one, 2013 - journals.plos.org
Genome data are becoming increasingly important for modern medicine. As the rate of
increase in DNA sequencing outstrips the rate of increase in disk storage capacity, the …

JARVIS3: an efficient encoder for genomic data

MJP Sousa, AJ Pinho, D Pratas - Bioinformatics, 2024 - academic.oup.com
Motivation Large-scale genomic projects grapple with the complex challenge of reducing
medium-and long-term storage space and its associated energy consumption, monetary …