Computational protocol: The bHLH transcription factor CgbHLH001 is a potential interaction partner of CDPK in halophyte Chenopodium glaucum

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Protocol publication

[…] The phylogenetic relationship of CDPK or bHLH transcription factors among various plant species was analyzed by using protein sequences from C. glaucum, Arabidopsis thaliana, Glycine max, Zea mays, Oryza sativa, etc. Multiple alignments were conducted with full-length amino acid sequence by Clustal W tool of MEGA 6.06. The phylogenetic tree was constructed through neighbor-joining (NJ) method of MEGA 6.06. Molecular distance of the aligned sequences was calculated according to the p-distance parameter, the gaps and missing data were treated as pairwise deletions. Branch points were tested by bootstrap with 1000 replicates. All amino acid sequences used in the present study were acquired from GenBank and Phytozome database. […]

Pipeline specifications

Software tools Clustal W, MEGA
Databases Phytozome
Application Phylogenetics
Organisms Nicotiana tabacum
Chemicals Calcium