Computational protocol: The Arabidopsis PLAT Domain Protein1 Is Critically Involved in Abiotic Stress Tolerance

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Protocol publication

[…] To identify members of the PLAT-plant-stress family from other plant species, multiple database searches were performed using the Basic Local Alignment Search Tool (BLAST) algorithms BLASTp and tBLASTn available on the public databases, PLAZA 2.0 (bioinformatics.psb.ugent.be/plaza) and Phytozome v8.0 (www.phytozome.net) with cutoff value of E<10−5. We used nucleotide and amino acid sequences of PLAT1 from the TAIR database (www.arabidopsis.org) to BLAST all databases. Phylogenetic analysis was performed by using CLUSTALW alignment in PHYLIP format clustal algorithm, and displayed in a phylogram tree format with locus name of each protein. Bootstrap values were presented as a percent of 100 resampled trees at each tree node using default settings of the TreeTop-Phylogenetic Tree (www.genebee.msu.su/services/phtreereduced.html). […]

Pipeline specifications

Software tools BLASTN, BLASTP, TBLASTN, Clustal W, PHYLIP
Databases TAIR Phytozome
Applications Phylogenetics, Amino acid sequence alignment
Organisms Arabidopsis thaliana
Chemicals Abscisic Acid, Triglycerides