Results 81 to 90 of about 24,640 (259)

De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing [version 2; referees: 1 approved, 3 approved with reservations]

F1000Research, 2018
Background: The introduction of the MinION sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. Nanopore sequence data offers great potential for de novo assembly of complex genomes without using other ...
Michael Liem, Hans J. Jansen, Ron P. Dirks, Christiaan V. Henkel, G. Paul H. van Heusden, Richard J.L.F. Lemmers, Trifa Omer, Shuai Shao, Peter J. Punt, Herman P. Spaink   +9 more
doaj   +1 more source

Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2 [PDF]

Genome Research, 2003
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes.
David B, Jaffe, Jonathan, Butler, Sante, Gnerre, Evan, Mauceli, Kerstin, Lindblad-Toh, Jill P, Mesirov, Michael C, Zody, Eric S, Lander   +7 more
openaire   +2 more sources

Dual native G‐quadruplex folding is associated with chromatin looping at the MYC locus

FEBS Open Bio, EarlyView.
BG4‐detectable G‐quadruplex (G4) in HaCaT and NHEK keratinocytes identified folded and unfolded G4s enriched at promoters/TSSs and active enhancers, whereas unfolded G4s also overlapped weak/poised enhancers. At MYC–PVT1, 3C‐qPCR detected enhancer–promoter looping only when G4s were simultaneously folded at both regulatory elements under native ...
Dieila Giomo de Lima, Gustavo Narvaes Guimarães, Emilyane de Oliveira Santana Amaral, Bianca Caroline Figueiredo Bianco, Manuel Jara‐Espejo, Sérgio Roberto Peres Line, Ana Paula de Souza, Aline Cristiane Planello   +7 more
wiley   +1 more source

A reference quality, fully annotated diploid genome from a Saudi individual

Scientific Data
We have used multiple sequencing approaches to sequence the genome of a volunteer from Saudi Arabia. We use the resulting data to generate a de novo assembly of the genome, and use different computational approaches to refine the assembly.
Maxat Kulmanov, Rund Tawfiq, Yang Liu, Hatoon Al Ali, Marwa Abdelhakim, Mohammed Alarawi, Hind Aldakhil, Dana Alhattab, Ebtehal A. Alsolme, Azza Althagafi, Angel Angelov, Salim Bougouffa, Patrick Driguez, Changsook Park, Alexander Putra, Ana M. Reyes-Ramos, Charlotte A. E. Hauser, Ming Sin Cheung, Malak S. Abedalthagafi, Robert Hoehndorf   +19 more
doaj   +1 more source

Improved Genome Sequence and Gene Annotation Resource for the Potato Late Blight Pathogen Phytophthora infestans

Molecular Plant-Microbe Interactions, 2020
Phytophthora infestans is a devastating pathogen causing potato late blight (Solanum tuberosum). Here we report the sequencing, assembly and genome annotation for two Phytophthora infestans isolates sampled in Republic of Korea.
Yoonyoung Lee, Kwang-Soo Cho, Jin-Hee Seo, Kee Hoon Sohn, Maxim Prokchorchik   +4 more
doaj   +1 more source

Avidin is evolutionarily conserved in fish but dispensable for development and resistance against Streptococcus agalactiae in zebrafish

FEBS Open Bio, EarlyView.
The presence of biotin‐binding avidin proteins in fish and their biological significance are poorly characterized. We cataloged fish avidins and demonstrate that they are widely present and evolutionarily conserved. We created avd knockout zebrafish and show that zebavidin is dispensable for development and that resistance of avd knockout embryos in ...
Anni K. Saralahti, Markus J. T. Ojanen, Mataleena Parikka, Otto Kauko, Mika Rämet, Vesa P. Hytönen   +5 more
wiley   +1 more source

Data Mining of the Coffee Rust Genome [PDF]

, 2012
The genomes of nine isolates of _Hemileia vastatrix_, the causal agent of coffee leaf rust were sequenced by Illumina and 454. Quality control, cleaning and _de novo_ assemblies of data were performed.
Silvia Restrepo, David Octavio Botero-Rozo, Alvaro Gaitan, Diego M. Riaño-Pachon, Marco Cristancho, William Giraldo   +5 more
core   +1 more source

diArk 2.0 provides detailed analyses of the ever increasing eukaryotic genome sequencing data

BMC Research Notes, 2011
Background Nowadays, the sequencing of even the largest mammalian genomes has become a question of days with current next-generation sequencing methods. It comes as no surprise that dozens of genome assemblies are released per months now.
Kollmar Martin, Hellkamp Marcel, Odronitz Florian, Hammesfahr Björn   +3 more
doaj   +1 more source

Salmonella enterica serovar typhi limits the potency of typhoid toxin and ADP‐ribosylating toxin AB to establish a persistent infection

FEBS Open Bio, EarlyView.
The two catalytic subunits of typhoid toxin dissociate from the holotoxin in the ER of an intoxicated cell, but only CdtB exits the ER to generate immunosuppressive effects. PltA is retained in the ER and sequestered from its cytosolic target, thus allowing the anti‐inflammatory effects of CdtB to promote intestinal colonization.
Maria C. Zabala‐Rodriguez, Juliette K. Tinker, Teresa Frisan, Taj Azarian, Ken Teter   +4 more
wiley   +1 more source

A minimal cellulosome‐like system in Cellulosilyticum lentocellum

FEBS Open Bio, EarlyView.
Cellulose‐degrading bacteria typically use cellulosomes, large multi‐enzyme complexes on a scaffold protein. In Cellulosilyticum lentocellum, we characterise a far smaller arrangement, a single scaffold bound to one cellulase through a single cohesin‐dockerin interaction.
John Allan, Amias Alstrom‐Moore, Gary W Black   +2 more
wiley   +1 more source