Computational protocol: The Pepper CaOSR1 Protein Regulates the Osmotic Stress Response via Abscisic Acid Signaling

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Protocol publication

[…] The encoded amino acid sequences for CaOSR1 and its homologs were obtained using BLAST searches (http://www.ncbi.nlm.nih.gov/BLAST). The amino acid alignment was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2), and the results were edited using Genedoc software (http://www.nrbsc.org/gfx/genedoc). The amino acid alignments were manually regulated to compare the cDNA clones of CaOSR1 with those of other organisms. Based on the data of multiple sequence alignment, phylogenetic tree was drawn with MEGA software (version 5.2). To investigate sequence identity and similarity between two proteins, pairwise sequence alignment was performed using EMBOSS Needle webtool (http://www.ebi.ac.uk/Tools/psa/emboss_needle) with default parameter. […]

Pipeline specifications

Software tools Clustal W, EMBOSS
Application Phylogenetics
Organisms Arabidopsis thaliana
Diseases Drug Hypersensitivity
Chemicals Abscisic Acid