Computational protocol: Integration analysis of MKK and MAPK family members highlights potential MAPK signaling modules in cotton

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Protocol publication

[…] The MKKs in Arabidopsis and O. sativa were used as queries to search for putative MKK proteins against the G. raimondii genome database at The PFAM ( and SMART ( databases were employed to detect conserved domains. The isoelectric points and molecular weights of the MKK proteins were predicted on the ExPASy proteomics server ( The subcellular localization of each MKK was analyzed using the CELLO v2.5 server ( Sequence alignment was carried out by the Clustal X program and a phylogenetic tree was constructed by the Maximum likelihood (ML) method in MEGA6. Mapping of MKK genes was performed using MapInspect ( Segment duplicates were identified using Plant Genome Duplication Database (http://chibba,, tandem duplicates were defined as genes separated by five or fewer genes. The exon/intron structures of individual MKK genes were determined by aligning the cDNA sequences to their corresponding genomic DNA sequences. […]

Pipeline specifications

Software tools CELLO, Clustal W, MEGA, MapComp
Databases Pfam PGDD Phytozome ExPASy
Applications Phylogenetics, Protein sequence analysis
Organisms Gossypium hirsutum, Gossypium raimondii, Arabidopsis thaliana