Global analysis of SNPs, proteins and protein-protein interactions: approaches for the prioritisation of candidate disease genes. [PDF]
, 2009 PhDUnderstanding the etiology of complex disease remains a challenge in biology. In recent years there has been an explosion in biological data, this study investigates machine learning and network analysis methods as tools to aid candidate disease ...
Dobson, Richard James Butler
core +4 more sources
GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level
G3: Genes, Genomes, Genetics, 2020 One of the most widely used programs for detecting positive selection, at the molecular level, is the program codeml, which is implemented in the Phylogenetic Analysis by Maximum Likelihood (PAML) package.
Laura G. Macías +2 more
doaj +1 more source
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
semanticscholar +1 more source
Exploring Protein Sequence Space Using Computationally Directed Recombination [PDF]
, 2006 Evolution has provided us with many protein sequences. However, these sequences represent a very small fraction of the possible sequences. In the laboratory, scientists have explored areas of sequence space not represented by natural proteins both to ...
Meyer, Michelle Margaret
core +1 more source
A sequence embedding method for enzyme optimal condition analysis
BMC Bioinformatics, 2020 Background An enzyme activity is influenced by the external environment. It is important to have an enzyme remain high activity in a specific condition.
Xiangjun Li +5 more
doaj +1 more source
Designing hardware for protein sequence analysis [PDF]
Bioinformatics, 2003 Abstract We present the architecture of PROSIDIS, a special purpose co-processor designed to search for the occurrence of substrings similar to a given ‘template string’ within a proteome. Actual tests show speed up figures ranging from 5 to 50 with respect to conventional general-purpose processors.
Alessandro Marongiu +2 more
openaire +4 more sources
STAR Protocols, 2023 Summary: Post-translational modifications (PTMs) serve as key regulatory mechanisms in various cellular processes; altered PTMs can potentially lead to human diseases.
Yu Yan +6 more
doaj +1 more source
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
HCMV Envelope Glycoprotein Diversity Demystified
Frontiers in Microbiology, 2019 Human cytomegalovirus (HCMV) is the leading viral cause of congenital birth defects and is responsible for morbidity and mortality in immunosuppressed individuals.
Mathilde Foglierini +3 more
doaj +1 more source
A protein structural study based on the centrality analysis of protein sequence feature networks.
PLoS ONE, 2021 In this paper, we use network approaches to analyze the relations between protein sequence features for the top hierarchical classes of CATH and SCOP. We use fundamental connectivity measures such as correlation (CR), normalized mutual information rate ...
Xiaogeng Wan, Xinying Tan
doaj +1 more source