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Organizing the bacterial annotation space with amino acid sequence embeddings
BackgroundDue to the ever-expanding gap between the number of proteins being discovered and their functional characterization, protein function...
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Investigating diversity and similarity between CBM13 modules and ricin-B lectin domains using sequence similarity networks
BackgroundThe CBM13 family comprises carbohydrate-binding modules that occur mainly in enzymes and in several ricin-B lectins. The ricin-B lectin...
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Ancestral Sequence Reconstruction and Alternate Amino Acid States Guide Protein Library Design for Directed Evolution
Engineered proteins possess nearly limitless possibilities in medical and industrial applications but finding a precise amino acid sequence for these...
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Signatures of T cell immunity revealed using sequence similarity with TCRDivER algorithm
Changes in the T cell receptor (TCR) repertoires have become important markers for monitoring disease or therapy progression. With the rise of...
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Broad Spectrum Amino Acid Racemases (Bsrs): A Potential Target in Microbial Research
Broad spectrum amino acid racemases (Bsrs) aid bacteria in producing non-canonical D-amino acids (NCDAA), which play significant functions in the...
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Functional annotation of a divergent genome using sequence and structure-based similarity
BackgroundMicrosporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high...
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Resource partitioning and amino acid assimilation in a terrestrial geothermal spring
High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in...
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FFP: joint Fast Fourier transform and fractal dimension in amino acid property-aware phylogenetic analysis
BackgroundAmino acid property-aware phylogenetic analysis (APPA) refers to the phylogenetic analysis method based on amino acid property encoding,...
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Clustering biological sequences with dynamic sequence similarity threshold
BackgroundBiological sequence clustering is a complicated data clustering problem owing to the high computation costs incurred for pairwise sequence...
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Amino acid profiles, amino acid sensors and transporters expression and intestinal microbiota are differentially altered in goats infected with Haemonchus contortus
Infection with the nematode Haemonchus contortus causes host malnutrition and gastrointestinal injuries. The objective of this study was to...
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Analysis of Multiple Protein Alignments Using 3D-Structural Information on the Orientation of Amino Acid Side-Chains
Multiple alignment of amino acid sequences of homologous proteins is a key tool in state-of-the-art bioinformatics and evolutionary analysis....
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Uncharacterized protein with amino acid deletions from Bombyx mori illustrates divergence from Bombyx mandarina hemocytin and showed modulated gene expression after infection by Nosema bombycis
Genome wide gene expression analysis, transcription analysis and mass spectrometry have revealed several uncharacterized genes and proteins from...
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Effects of the kinetic pattern of dietary glucose release on nitrogen utilization, the portal amino acid profile, and nutrient transporter expression in intestinal enterocytes in piglets
BackgroundPromoting the synchronization of glucose and amino acid release in the digestive tract of pigs could effectively improve dietary nitrogen...
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Identifying host-specific amino acid signatures for influenza A viruses using an adjusted entropy measure
BackgroundInfluenza A viruses (IAV) exhibit vast genetic mutability and have great zoonotic potential to infect avian and mammalian hosts and are...
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Enzyme Modeling: From the Sequence to the Substrate Complex
This chapter gives an overview on computational methods to study the relationship between sequence, structure, and function of proteins....
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Amino acid insertion in Bat MHC-I enhances complex stability and augments peptide presentation
Bats serve as reservoirs for numerous zoonotic viruses, yet they typically remain asymptomatic owing to their unique immune system. Of particular...
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Metabuli: sensitive and specific metagenomic classification via joint analysis of amino acid and DNA
Metagenomic taxonomic classifiers analyze either DNA or amino acid (AA) sequences. Metabuli ( https://metabuli.steineggerlab.com ), however, jointly...
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Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
Codon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino...
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Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation
Ancestral sequence reconstruction (ASR) is a phylogenetic method widely used to analyze the properties of ancient biomolecules and to elucidate...
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The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi
BackgroundScab, caused by the biotrophic fungus Venturia inaequalis , is the most economically important disease of apples worldwide. During...
