Computational protocol: The membrane tethered transcription factor EcbZIP17 from finger millet promotes plant growth and enhances tolerance to abiotic stresses

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Protocol publication

[…] For nucleotide and protein sequence analysis, the National Centre for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/) was used. The basic leucine zipper (BRLZ) and transmembrane domains in EcbZIP17 were observed using the Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de/). The leucine rich nuclear export signals (NES) were predicted by the NetNES 1.1 server (http://www.cbs.dtu.dk/services/NetNES/), whereas the nuclear localisation signal was predicted by the cNLS Mapper tool (http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi). The CELLO 2.5 Sub-Cellular Localisation predictor (http://cello.life.nctu.edu.tw/) was used for subcellular localisation. The alignment analysis of EcbZIP17 and its homologs obtained from related species was carried out using CLUSTALW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/), and the phylogenetic tree was constructed using MEGA 5.0. The Multiple EM for Motif Elicitation software (MEME; http://meme-suite.org/tools/meme) was used for identifying motifs present in CLUSTALW2 aligned sequences. […]

Pipeline specifications

Software tools NetNES, cNLS Mapper, CELLO, Clustal W, MEME, MEME Suite
Databases SMART
Applications Phylogenetics, Protein sequence analysis
Organisms Nicotiana tabacum
Diseases Machado-Joseph Disease
Chemicals Mannitol, Polyethylene Glycols, Sodium Chloride