Results 51 to 60 of about 141,521 (289)

Robust structure measures of metabolic networks that predict prokaryotic optimal growth temperature

BMC Bioinformatics, 2019
Background Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism.
Adèle Weber Zendrera, Nataliya Sokolovska, Hédi A. Soula   +2 more
doaj   +1 more source

Draft genome sequence of Colletotrichum acutatum sensu lato (Colletotrichum fioriniae) [PDF]

, 2014
In addition to its economic impact, Colletotrichum acutatum sensu lato is an interesting model for molecular investigations due to the diversity of host-determined specialization and reproductive lifestyles within the species complex.
Holub, Eric, Sreenivasaprasad, Prasad, Sukno, Serenella A., Sreenivasaprasad, S., Thon, M. R., Holub, E. B., Sukno, S. A., Baroncelli, Riccardo, Thon, Michael R.   +8 more
core   +1 more source

Genome Graphs [PDF]

, 2011
Whole-genome shotgun sequencing is an experimental technique used for obtaining information about a genome’s sequence, whereby it is broken up into many short (possibly overlapping) segments whose sequence is then determined.
Medvedev, Paul
core   +3 more sources

SPAligner: alignment of long diverged molecular sequences to assembly graphs

BMC Bioinformatics, 2020
Background Graph-based representation of genome assemblies has been recently used in different contexts — from improved reconstruction of plasmid sequences and refined analysis of metagenomic data to read error correction and reference-free haplotype ...
Tatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov, Sergey Nurk   +3 more
doaj   +1 more source

JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures. [PDF]

PLoS ONE, 2017
Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly
Jieming Shi, Xi Li, Min Dong, Mitchell Graham, Nehul Yadav, Chun Liang   +5 more
doaj   +1 more source

Mosaic Graphs and Comparative Genomics in Phage Communities [PDF]

Journal of Computational Biology, 2010
Comparing the genomes of two closely related viruses often produces mosaics where nearly identical sequences alternate with sequences that are unique to each genome. When several closely related genomes are compared, the unique sequences are likely to be shared with third genomes, leading to virus mosaic communities.
Mahdi Belcaid, Anne Bergeron, Guylaine Poisson   +2 more
openaire   +2 more sources

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies [PDF]

, 2014
Background: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O.
Moreau, Hervé, Van De Peer, Yves, Adam Eyre-Walker, Château, Annie, Van de Peer, Y., Stephane Rombauts, Carré, Isabelle, Eyre-Walker, Adam, Rivals, E., Peer, Yves van de, Wendy Schackwitz, Schackwitz, Wendy, Benoit Piégu, Moreau, H., Schackwitz, W., Grimsley, Nigel, Evelyne Derelle, Rombauts, Stephane, Eyre Walker, Adam, Blanc-Mathieu, R., Eyre-Walker, A., Verhelst, B., Blanc-Mathieu, Romain, Bouget, François-Yves, Hervé Moreau, Nigel Grimsley, Rivals, Eric, Piégu, Benoit, Isabelle Carré, François-Yves Bouget, Derelle, Evelyne, Eric Rivals, Carré, I., Gwenaël Piganeau, Derelle, E., Bram Verhelst, Verhelst, Bram, Annie Château, Romain Blanc-Mathieu, Bouget, F.-Y., Château, A., Carré, Isabelle A., Piégu, B., Grimsley, N., Piganeau, G., Rombauts, S., Piganeau, Gwenaël, Blanc Mathieu, Romain, Yves Van de Peer   +48 more
core   +1 more source

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting. [PDF]

, 2014
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infection. Whole-genome sequencing of MRSA has been used to define phylogeny and transmission in well-resourced healthcare settings, yet the greatest burden of nosocomial ...
Thaipadungpanit, J, Holden, MTG, Cauchemez, S, Jombart, Thibaut, Tong, SY, Nickerson, Emma K, Hongsuwan, M, Cori, A, Cauchemez, Simon, Holden, Matthew T G, Parkhill, J, Köser, CU, Tong, SYC, Nickerson, EK, Day, Nicholas P, Day, NP, Holden, MT, Fraser, C, Tong, Steven Y C, Fraser, Christophe, Limmathurotsakul, Direk, Limmathurotsakul, D, Cooper, Ben, Wuthiekanun, Vanaporn, Peacock, SJ, Köser, Claudio U, Wuthiekanun, V, Cooper, BS, Cori, Anne, Parkhill, Julian, Cooper, Ben S, Day, Nicholas, Thaipadungpanit, Janjira, Peacock, Sharon J, Jombart, T, Hongsuwan, Maliwan   +35 more
core   +2 more sources

Unitig level assembly graph based metagenome-assembled genome refiner (UGMAGrefiner): A tool to increase completeness and resolution of metagenome-assembled genomes

Computational and Structural Biotechnology Journal, 2023
De novo assembly of next generation metagenomic reads is widely used to provide taxonomic and functional information of genomes in a microbial community.
Baoyu Xiang, Liping Zhao, Menghui Zhang
doaj   +1 more source

A graph-based approach to diploid genome assembly [PDF]

Bioinformatics, 2018
Abstract Motivation Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in health and disease. Current assembly approaches often collapse the two sequences into one haploid consensus sequence
Shilpa Garg, Mikko Rautiainen, Adam M. Novak, Erik Garrison, Richard Durbin, Tobias Marschall   +5 more
openaire   +3 more sources