Integrating sequence and structural biology with DAS [PDF]
BMC Bioinformatics, 2007 Background The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence.
Finn Robert D +5 more
doaj +7 more sources
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence [PDF]
Nature, 1998 Stewart T. Cole +41 more
openalex +2 more sources
Strainberry: automated strain separation in low-complexity metagenomes using long reads
Nature Communications, 2021 Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and ...
Riccardo Vicedomini +3 more
doaj +1 more source
decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
Microbiome, 2023 Background The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources.
Camila Duitama González +5 more
doaj +1 more source
Mapping-friendly sequence reductions: Going beyond homopolymer compression
iScience, 2022 Summary: Sequencing errors continue to pose algorithmic challenges to methods working with sequencing data. One of the simplest and most prevalent techniques for ameliorating the detrimental effects of homopolymer expansion/contraction errors present in ...
Luc Blassel, Paul Medvedev, Rayan Chikhi
doaj +1 more source
Predicting multiple conformations via sequence clustering and AlphaFold2
Nature, 2023 AlphaFold2 (ref. 1) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein’s biological function often depends on multiple conformational substates2, and disease-causing point mutations often ...
Hannah K. Wayment-Steele +8 more
semanticscholar +1 more source
Mega-scale experimental analysis of protein folding stability in biology and design
Nature, 2023 Large-scale assays using cDNA display proteolysis are used to measure the folding stabilities of protein domains, providing a method to quantify the effects of mutations on protein folding, with applications in protein design.
Kotaro Tsuboyama +8 more
semanticscholar +1 more source
SaPt-CNN-LSTM-AR-EA: a hybrid ensemble learning framework for time series-based multivariate DNA sequence prediction [PDF]
PeerJ, 2023 Biological sequence data mining is hot spot in bioinformatics. A biological sequence can be regarded as a set of characters. Time series is similar to biological sequences in terms of both representation and mechanism.
Wu Yan +5 more
doaj +2 more sources
HostPhinder: A Phage Host Prediction Tool
Viruses, 2016 The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput ...
Julia Villarroel +6 more
doaj +1 more source
BERTology Meets Biology: Interpreting Attention in Protein Language Models [PDF]
bioRxiv, 2020 Transformer architectures have proven to learn useful representations for protein classification and generation tasks. However, these representations present challenges in interpretability.
Jesse Vig +5 more
semanticscholar +1 more source