Computational protocol: Mechanism of internal browning of pineapple: The role of gibberellins catabolism gene (AcGA2ox) and GAs

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Protocol publication

[…] DNA sequence data were analyzed using the programs provided by the National Centre of Biotechnology (NCBI) web site (http://www.ncbi.nlm.nih.gov). The BLASTN and BLASTP programs were used for the gene sequence homology search. Amino acid sequences of selected plant GA-2oxidase genes were aligned using ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/). A phylogenetic tree was constructed using maximum parsimony with 500 bootstrap replicates of MEGA6.06. ExPASy web site (http://cn.expasy.org/tools/) and programs therein were used for the prediction of amino acid features of AcGA2ox. […]

Pipeline specifications

Software tools BLASTN, BLASTP, Clustal W, MEGA
Databases ExPASy
Application Phylogenetics
Organisms Ananas comosus, Arabidopsis thaliana
Chemicals Abscisic Acid, Gibberellins