Computational protocol: Overexpression of the Starch Phosphorylase-Like Gene (PHO3) in Lotus japonicus has a Profound Effect on the Growth of Plants and Reduction of Transitory Starch Accumulation

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Protocol publication

[…] Sequences of PHO proteins were retrieved from GenBank. Arabidopsis PHO proteins were used as queries in BLAST searches against the L. japonicus genome database. Conserved motifs in PHO proteins were analyzed using the NCBI’s CDD database (). The plastid transit peptide cleavage site of the PHO proteins was predicted using the program TargetP Server v1.01 (). For phylogenetic analysis, multiple sequence alignments of PHO amino acid sequences were performed using ClustalW. The tree was constructed using the neighbor-joining (NJ) method and 100 bootstraps in order to group putative full-length PHO amino acid sequences, and the results were displayed with Mega software version 4 (). […]

Pipeline specifications

Software tools TargetP, Clustal W, MEGA
Applications Phylogenetics, Protein sequence analysis
Organisms Lotus japonicus, Branchiostegus japonicus