Results 51 to 60 of about 4,751,605 (346)

A high-throughput protocol for deamination of long single-stranded DNA and oligo pools containing complex sequences

STAR Protocols, 2023
Summary: Cytidine deaminases as DNA mutators play important roles in immunity and genome stability. Here, we present a high-throughput protocol for deamination of long single-stranded (ss) DNA or oligo pools containing complex sequences.
Yanyan Wang, Senxin Zhang, Xiaoqi Zheng, Leng-Siew Yeap, Fei-Long Meng   +4 more
doaj   +1 more source

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

BMC Biology, 2014
BackgroundThe study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics.
S. Salter, M. Cox, E. Turek, S. Calus, W. Cookson, M. Moffatt, P. Turner, J. Parkhill, N. Loman, A. Walker   +9 more
semanticscholar   +1 more source

FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses

Journal of Immunology Research, 2015
FluKB is a knowledge-based system focusing on data and analytical tools for influenza vaccine discovery. The main goal of FluKB is to provide access to curated influenza sequence and epitope data and enhance the analysis of influenza sequence diversity ...
Christian Simon, Ulrich J. Kudahl, Jing Sun, Lars Rønn Olsen, Guang Lan Zhang, Ellis L. Reinherz, Vladimir Brusic   +6 more
doaj   +1 more source

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

Journal of Molecular Biology, 1999
An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as ...
D. Mathews, Jeffrey Sabina, M. Zuker, D. Turner   +3 more
semanticscholar   +1 more source

occumb: An R package for site occupancy modeling of eDNA metabarcoding data

Population Ecology, EarlyView.
This study introduces a new R package, occumb, for the convenient application of site occupancy modeling using environmental DNA (eDNA) metabarcoding data. We outline a data analysis workflow, including data setup, model fitting, model assessment, and comparison of potential study settings based on model predictions, all of which can be performed using
Keiichi Fukaya, Yuta Hasebe
wiley   +1 more source

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Bioinform., 2009
Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file
P. Cock, T. Antão, Jeffrey T. Chang, Brad A. Chapman, C. Cox, A. Dalke, Iddo Friedberg, T. Hamelryck, F. Kauff, B. Wilczyński, Michiel J. L. de Hoon   +10 more
semanticscholar   +1 more source

Representation learning applications in biological sequence analysis

bioRxiv, 2021
Remarkable advances in high-throughput sequencing have resulted in rapid data accumulation, and analyzing biological (DNA/RNA/protein) sequences to discover new insights in biology has become more critical and challenging.
Hitoshi Iuchi, Taro Matsutani, Keisuke Yamada, Natsuki Iwano, Shunsuke Sumi, S. Hosoda, Shitao Zhao, Tsukasa Fukunaga, Michiaki Hamada   +8 more
semanticscholar   +1 more source

Fungal genome sequencing: basic biology to biotechnology [PDF]

Critical Reviews in Biotechnology, 2015
The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s.
openaire   +3 more sources

Sequencing the Biology of Entry: The Retroviral env Gene [PDF]

, 2017
The surface envelope protein of any virus is major determinant of the host cell that is infected and as a result a major determinant of viral pathogenesis. Retroviruses have a single surface protein named Env. It is a trimer of heterodimers and is responsible for binding to the host cell receptor and mediating fusion between the viral and host ...
Shuntai Zhou, Ronald Swanstrom, William D. Graham   +2 more
openaire   +3 more sources

Infection Models for Pine Wilt Disease on the Basis of Vector Behaviors

Population Ecology, EarlyView.
Infection models for pine wilt disease without vector density were built to estimate the transmission coefficient of the pathogenic nematode. The models successfully simulated the annual change in the density of infected trees for four pine stands. ABSTRACT Pine wilt disease is caused by the pinewood nematode (Bursaphelenchus xylophilus Steiner et ...
Katsumi Togashi
wiley   +1 more source