Results 31 to 40 of about 3,888,779 (212)
Analysis of protein-coding genetic variation in 60,706 humans
Nature, 2015 Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data ...
James Y. Zou
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MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
Nature Biotechnology, 2017 VOLUME 35 NUMBER 11 NOVEMBER 2017 NATURE BIOTECHNOLOGY performance was to combine the doublematch criterion with making k-mers as long as possible, which required finding similar and not just exact k-mers. This effectively bases our decision on up to 2 ×
Martin Steinegger, J. Söding
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BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data
Biology Direct, 2022 Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes ...
Markus Sutter, Cheryl A. Kerfeld
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iScience, 2021 Summary: Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations
Keisuke Motone +2 more
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Filtering Degenerate Patterns with Application to Protein Sequence Analysis
Algorithms, 2013 In biology, the notion of degenerate pattern plays a central role for describing various phenomena. For example, protein active site patterns, like those contained in the PROSITE database, e.g., [FY ]DPC[LIM][ASG]C[ASG], are, in general, represented by ...
Matteo Comin, Davide Verzotto
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MethodsX, 2022 The wealth of sequence data available on public databases is increasing at an exponential rate, and while tremendous efforts are being made to make access to these resources easier, these data can be challenging for researchers to reuse because ...
Kyra Dougherty, Katalin A. Hudak
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The Phylogeny of Osteopontin—Analysis of the Protein Sequence [PDF]
International Journal of Molecular Sciences, 2018 Osteopontin (OPN) is important for tissue remodeling, cellular immune responses, and calcium homeostasis in milk and urine. In pathophysiology, the biomolecule contributes to the progression of multiple cancers. Phylogenetic analysis of 202 osteopontin protein sequences identifies a core block of integrin-binding sites in the center of the protein ...
openaire +3 more sources
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
Molecular Systems Biology, 2011 Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets
Fabian Sievers +11 more
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A Protein Sequence Analysis Hardware Accelerator Based on Divergences
International Journal of Reconfigurable Computing, 2012 The Viterbi algorithm is one of the most used dynamic programming algorithms for protein comparison and identification, based on hidden markov Models (HMMs).
Juan Fernando Eusse +3 more
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MMseqs2: sensitive protein sequence searching for the analysis of massive data sets
bioRxiv, 2017 Sequencing costs have dropped much faster than Moore's law in the past decade, and sensitive sequence searching has become the main bottleneck in the analysis of large (meta)genomic datasets. While previous methods sacrificed sensitivity for speed gains,
Martin Steinegger, J. Söding
semanticscholar +1 more source