Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

SF Altschul, TL Madden, AA Schäffer… - Nucleic acids …, 1997‏ - academic.oup.com
The BLAST programs are widely used tools for searching protein and DNA databases for
sequence similarities. For protein comparisons, a variety of definitional, algorithmic and …

Recent developments in the MAFFT multiple sequence alignment program

K Katoh, H Toh - Briefings in bioinformatics, 2008‏ - academic.oup.com
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins
have long been and are still important issues in bioinformatics. To rapidly construct a …

Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism

T Vatanen, KS Jabbar, T Ruohtula, J Honkanen… - Cell, 2022‏ - cell.com
The perinatal period represents a critical window for cognitive and immune system
development, promoted by maternal and infant gut microbiomes and their metabolites. Here …

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

SH Yoon, SM Ha, S Kwon, J Lim… - … of systematic and …, 2017‏ - microbiologyresearch.org
The recent advent of DNA sequencing technologies facilitates the use of genome
sequencing data that provide means for more informative and precise classification and …

[HTML][HTML] VSEARCH: a versatile open source tool for metagenomics

T Rognes, T Flouri, B Nichols, C Quince, F Mahé - PeerJ, 2016‏ - peerj.com
Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for
processing and preparing metagenomics, genomics and population genomics nucleotide …

ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences

I Lee, M Chalita, SM Ha, SI Na… - … of systematic and …, 2017‏ - microbiologyresearch.org
Thanks to the recent advancement of DNA sequencing technology, the cost and time of
prokaryotic genome sequencing have been dramatically decreased. It has repeatedly been …

The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study

LG Jang, G Choi, SW Kim, BY Kim, S Lee… - Journal of the …, 2019‏ - Taylor & Francis
Background Recently, gut microbiota have been studied extensively for health promotion,
disease prevention, disease treatment, and exercise performance. It is recommended that …

Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species

OS Kim, YJ Cho, K Lee, SH Yoon… - … of systematic and …, 2012‏ - microbiologyresearch.org
Despite recent advances in commercially optimized identification systems, bacterial
identification remains a challenging task in many routine microbiological laboratories …

GenASM: A high-performance, low-power approximate string matching acceleration framework for genome sequence analysis

DS Cali, GS Kalsi, Z Bingöl, C Firtina… - 2020 53rd Annual …, 2020‏ - ieeexplore.ieee.org
Genome sequence analysis has enabled significant advancements in medical and scientific
areas such as personalized medicine, outbreak tracing, and the understanding of evolution …

TNF dually mediates resistance and susceptibility to mycobacteria via mitochondrial reactive oxygen species

FJ Roca, L Ramakrishnan - Cell, 2013‏ - cell.com
Tumor necrosis factor (TNF) constitutes a critical host defense against tuberculosis, but its
excess is also implicated in tuberculosis pathogenesis in zebrafish and humans. Using the …