Phylogenetic tree building in the genomic age
Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …
A brief history of bioinformatics
J Gauthier, AT Vincent, SJ Charette… - Briefings in …, 2019 - academic.oup.com
It is easy for today's students and researchers to believe that modern bioinformatics
emerged recently to assist next-generation sequencing data analysis. However, the very …
emerged recently to assist next-generation sequencing data analysis. However, the very …
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
K Katoh, J Rozewicki, KD Yamada - Briefings in bioinformatics, 2019 - academic.oup.com
This article describes several features in the MAFFT online service for multiple sequence
alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers …
alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers …
The clustal omega multiple alignment package
F Sievers, DG Higgins - Multiple sequence alignment: Methods and …, 2021 - Springer
Clustal Omega is a version, completely rewritten and revised in 2011, of the widely used
Clustal series of programs for multiple sequence alignment. It can deal with very large …
Clustal series of programs for multiple sequence alignment. It can deal with very large …
DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes
J Pfab, NM Phan, D Si - Proceedings of the National …, 2021 - National Acad Sciences
Information about macromolecular structure of protein complexes and related cellular and
molecular mechanisms can assist the search for vaccines and drug development processes …
molecular mechanisms can assist the search for vaccines and drug development processes …
[HTML][HTML] Protein secondary structure prediction using deep convolutional neural fields
Protein secondary structure (SS) prediction is important for studying protein structure and
function. When only the sequence (profile) information is used as input feature, currently the …
function. When only the sequence (profile) information is used as input feature, currently the …
A simple method to control over-alignment in the MAFFT multiple sequence alignment program
K Katoh, DM Standley - Bioinformatics, 2016 - academic.oup.com
Motivation: We present a new feature of the MAFFT multiple alignment program for
suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly …
suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly …
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 …
MAFFT multiple sequence alignment software version 7: improvements in performance and usability
K Katoh, DM Standley - Molecular biology and evolution, 2013 - academic.oup.com
We report a major update of the MAFFT multiple sequence alignment program. This version
has several new features, including options for adding unaligned sequences into an existing …
has several new features, including options for adding unaligned sequences into an existing …
[HTML][HTML] Gut microbiome function predicts response to anti-integrin biologic therapy in inflammatory bowel diseases
The gut microbiome plays a central role in inflammatory bowel diseases (IBDs)
pathogenesis and propagation. To determine whether the gut microbiome may predict …
pathogenesis and propagation. To determine whether the gut microbiome may predict …