Results 121 to 130 of about 4,504,319 (408)
SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
PLoS ONE, 2014 The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that
Brejnev Muhire, A. Varsani, D. Martin
semanticscholar +1 more source
Protein Sequence Alignment Techniques [PDF]
Acta Crystallographica Section D Biological Crystallography, 1998 The basic algorithms for alignment of two or more protein sequences are explained. Alternative methods for scoring substitutions and gaps (insertions and deletions) are described, as are global and local alignment methods. Multiple alignment techniques are explained, including methods for profile comparison.
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Molecular Oncology, EarlyView.The authors applied joint/mixed models that predict mortality of trifluridine/tipiracil‐treated metastatic colorectal cancer patients based on circulating tumor DNA (ctDNA) trajectories. Patients at high risk of death could be spared aggressive therapy with the prospect of a higher quality of life in their remaining lifetime, whereas patients with a ...
Matthias Unseld +7 more
wiley +1 more source
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
BMC Bioinformatics, 2003 Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of ...
Searle Stephen MJ +4 more
doaj +1 more source
HQAlign: Aligning nanopore reads for SV detection using current-level modeling [PDF]
arXiv, 2023 Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate alignment of these long reads play an important role in identifying novel SVs.
arxiv
A simple method to control over-alignment in the MAFFT multiple sequence alignment program
Bioinform., 2016 Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over ...
K. Katoh, D. Standley
semanticscholar +1 more source
Molecular Oncology, EarlyView.Tumor microenvironment drives cancer formation and progression. We analyzed the role of human cancer‐associated adipocytes from patients with renal cell carcinoma (RCC) stratified as lean, overweight, or obese. RNA‐seq demonstrated that, among the most altered genes involved in the tumor–stroma crosstalk, are ADAM12 and CYP1B1, which were proven to be ...
Sepehr Torabinejad +13 more
wiley +1 more source
Topological network alignment uncovers biological function and phylogeny
, 2009 Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact.
Cook S. +15 more
core +2 more sources
Sequence alignment for molecular replacement [PDF]
Acta Crystallographica Section D Biological Crystallography, 2007 This article focuses on the key step of obtaining the best possible sequence alignment of the Query (the protein you are interested in) to the Target (a protein of known three-dimensional structure) in order to build a molecular model for molecular replacement. Common sequence-alignment methods are discussed, starting from structural alignment and then
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Molecular Oncology, EarlyView.Large multidimensional digital images of cancer tissue are becoming prolific, but many challenges exist to automatically extract relevant information from them using computational tools. We describe publicly available resources that have been developed jointly by expert and non‐expert computational biologists working together during a virtual hackathon
Sandhya Prabhakaran +16 more
wiley +1 more source