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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 …
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 …
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 …
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
The recent advent of DNA sequencing technologies facilitates the use of genome
sequencing data that provide means for more informative and precise classification and …
sequencing data that provide means for more informative and precise classification and …
[HTML][HTML] VSEARCH: a versatile open source tool for metagenomics
Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for
processing and preparing metagenomics, genomics and population genomics nucleotide …
processing and preparing metagenomics, genomics and population genomics nucleotide …
ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences
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 …
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
Background Recently, gut microbiota have been studied extensively for health promotion,
disease prevention, disease treatment, and exercise performance. It is recommended that …
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
Despite recent advances in commercially optimized identification systems, bacterial
identification remains a challenging task in many routine microbiological laboratories …
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
Genome sequence analysis has enabled significant advancements in medical and scientific
areas such as personalized medicine, outbreak tracing, and the understanding of evolution …
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 …
excess is also implicated in tuberculosis pathogenesis in zebrafish and humans. Using the …