CAUSA 2.0: accurate and consistent evolutionary analysis of proteins using codon and amino acid unified sequence alignments

Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)

An Evolutionary Relationship Between Stearoyl-CoA Desaturase (SCD) Protein Sequences Involved in Fatty Acid Metabolism

Background: Stearoyl-CoA desaturase (SCD) is a key enzyme that converts saturated fatty acids (SFAs) to monounsaturated fatty acids (MUFAs) in fat biosynthesis. Despite being crucial for interpreting SCDs’ roles across species, the evolutionary relationship of SCD proteins across species has yet to be elucidated. This study aims to present this evolutionary relationship based on amino aci...

Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates

Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN∕dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it assigns a relative conservation score to each site in an alignment. How site-wise dN∕dS values relate to Rate4Site scores is not known...

Molecular Characterization of a Three-disulfide Bridges Beta-like Neurotoxin from Androctonus crassicauda Scorpion Venom

Scorpion venom is the richest source of peptide toxins with high levels of specific interactions with different ion-channel membrane proteins. The present study involved the amplification and sequencing of a 310-bp cDNA fragment encoding a beta-like neurotoxin active on sodium ion-channel from the venom glands of scorpion Androctonus crassicauda belonging to the Buthidae family using r...

Investigation of Solvent Effect on CUA Codon Mutation: NMR Shielding Study

P53 is one of the gene that has important role in human cell cycle and in the human cancers too.Models of codon substitution make it possible to separate mutational biases in the DNA fromselective constraints on the protein, and offer a great advantage over amino acid models forunderstanding the evolutionary process of proteins and protein-coding DNA sequences. In thiswork, we investigated abou...