Computational protocol: Cloning, expression and characterization of COI1 gene (AsCOI1) from Aquilaria sinensis (Lour.) Gilg

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Protocol publication

[…] The sequence encoding AsCOI1 was determined by homology searches in the NCBI databases using the BLAST program, and the homology sequences were downloaded from these databases. The alignment of the AsCOI1 protein with other structurally-related COI1 proteins was performed using the Clustal X program. Some other bioinformatic sequence features of AsCOI1, such as molecular weight (MW), theoretical isoelectric point (pI) and stability, were determined as described. The cNLS Mapper (http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi) was used to predict the nuclear localization signals. Conserved motifs of COI1s in A. sinensis and other species were analyzed using Multiple Expectation Maximization for Motif Elicitation (MEME) version 4.9.1 with the following parameters. Optimum motif width was set to ≥6 and ≤50. The conserved residues were analyzed by aligning amino acid sequences using T-coffee and by searching literature references. SWISS-MODEL was used to analyze the molecular modeling of AsCOI1 protein.To determine the relationship between AsCOI1 and other COI1 proteins, phylogenetic analysis was constructed for 16 COI1 proteins of different species using MEGA version 5.05 by the neighbor-joining method with 1000 bootstrap replicates. […]

Pipeline specifications

Software tools Clustal W, cNLS Mapper, MEME, T-Coffee, MEGA
Applications Phylogenetics, Protein sequence analysis
Organisms Aquilaria sinensis
Chemicals Amino Acids