Computational protocol: Serine carboxypeptidase 46 Regulates Grain Filling and Seed Germination in Rice (Oryza sativa L.)

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Protocol publication

[…] The information regarding the SCP genomic sequence, CDS sequence and protein sequence was downloaded from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/). The sequence of maize SCPL gene family was downloaded from MaizeGDB (http://www.maizegdb.org/). The numbers of the SCPL gene family were analyzed by ClustalW (MEGA 7.0). The phylogenetic tree was constructed in MEGA7.0 using the Maximum Likelihood. The evolutionary distances were computed using the Jones-Taylor-Thornton (JTT) model, and the substitutions type was amino acid. There were about 1,000 replicates performed in each analysis in the bootstrap test to obtain confidence support. The ML tree was searched using the Nearest-Neighbor-Interchange (NNI). The branch length scale bar indicates the evolutionary distance. […]

Pipeline specifications

Software tools Clustal W, MEGA
Databases MaizeGDB RGAP
Application Phylogenetics
Organisms Oryza sativa