Similar protocols

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 http://www.phytozome.net. The PFAM (http://pfam.sanger.ac.uk) and SMART (http://smart.emblheidelberg.de/) databases were employed to detect conserved domains. The isoelectric points and molecular weights of the MKK proteins were predicted on the ExPASy proteomics server (http://expasy.org/). The subcellular localization of each MKK was analyzed using the CELLO v2.5 server (http://cello.life.nctu.edu.tw/). 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 (http://www.plantbreeding.wur.nl/UK/software_mapinspect.html). Segment duplicates were identified using Plant Genome Duplication Database (http://chibba,agtec.uga.edu/duplication), 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
Organisms Gossypium hirsutum, Gossypium raimondii, Arabidopsis thaliana