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CastNet: a systems-level sequence evolution simulator
BackgroundSimulating DNA evolution has been done through coevolution-agnostic probabilistic frameworks for the past 3 decades. The most common...
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SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies
BackgroundSimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well...
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GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2
BackgroundDespite GC variation constitutes a fundamental element of genome and species diversity, the precise mechanisms driving it remain unclear....
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Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution
The complex and bioactive monoterpene indole alkaloids (MIAs) found in Catharanthus roseus and related species are the products of many millions of...
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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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Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus
BackgroundThe genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD)....
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Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids
BackgroundN6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between...
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Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships
The chloroplast (cp) genome holds immense potential for a variety of applications including species identification, phylogenetic analysis, and...
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Sequence Alignment
New biological sequences do not emerge de novo in nature but rather are derived from pre-existing sequences. This foundational principle underlies...
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Chunking as a function of sequence length
Chunking mechanisms are central to several cognitive processes. During the acquisition of visuo-motor sequences, it is commonly reported that these...
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Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex
Key messageReplacing the native clpP1 gene in the Nicotiana plastid genome with homologs from different donor species showed that the extent of...
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Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding
BackgroundRepetitive DNA sequences accounts for over 80% of maize genome. Although simple sequence repeats (SSRs) account for only 0.03% of the...
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Predicting subcellular location of protein with evolution information and sequence-based deep learning
BackgroundProtein subcellular localization prediction plays an important role in biology research. Since traditional methods are laborious and...
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Genome evolution: Lessons from Genolevures
In the past years, yeast genome-sequencing programs have been widely developed. Two of them, namely Genolevures I and II, were devoted to the...
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The Structural Biology of Catalase Evolution
Catalases are essential enzymes for removal of hydrogen peroxide, enabling aerobic and anaerobic metabolism in an oxygenated atmosphere....
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The evolution of chikungunya virus circulating in Indonesia: Sequence analysis of the orf2 gene encoding the viral structural proteins
Chikungunya virus (CHIKV) is an arthropod-borne virus that has caused several major epidemics globally, including in Indonesia. Although significant...
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Sequence-structural features and evolution of the α-amylase family GH119 revealed by the in silico analysis of its relatedness to the family GH57
In the sequence-based classification of glycoside hydrolases (GHs) of the CAZy database, the family GH119 represents one of the four α-amylase GH...
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Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons
The DNA methyltransferase DNMT3C appeared as a duplication of the DNMT3B gene in muroids and is required for silencing of young retrotransposons in...
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Convergent Evolution Animal Form and Function
This volume presents a series of case studies, at different levels of inclusivity, of how organisms exhibit functional convergence as a key...