Pipeline publication

[…] ClustalW with default parameters. A phylogenetic tree was constructed using MEGA 5.0, comparing 47 Arabidopsis thaliana Dof domains using the neighbor-joining method with a bootstrap value of 1,000 [61,62]., Several physiological and biochemical indices were also analyzed. The theoretical pI was calculated by ExPASy (http://web.expasy.org/compute_pi/) [63]. Sequence Manipulation Suite (http://www.bio-soft.net/sms/) was used to analyze protein statistics, and the solubility of recombinant proteins was predicted by the RPSP program (http://biotech.ou.edu) [64]. The synteny of the BraDof genes was calculated by MicroSyn software according to Cai’s means (http://fcsb.njau.edu.cn/microsyn/) [65]., OrthoMCL was used to search for orthologous and paralogous genes in Chinese cabbage, Arabidopsis, and rice using the entire Dof protein sequences [66]. We used an E-value of 1e−5 for BLASTP and OrthoMCL analyses, gathered the orthologous and paralogous relationships, and displayed them using the Circos software (http://circos.ca/) [67]. An interaction network of BraDof genes from Chinese cabbage was constructed to understand the genome-wide regulation network. An interaction work of Arabidopsis Dof proteins was constructed using the Arabidopsis Interactions Viewer (http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi). By replacing Arabidopsis proteins with corresponding orthologous and co-orthologous Chinese cabbage proteins, an interaction network of BraDof proteins from Chinese cabbage was constructed and displayed using the Cytoscape software (http://www.cytoscape.org/)., Seeds of ‘Lubaisanhao’ and ‘Qingdao87-114’ were obtained from the State Key Laboratory […]

Pipeline specifications

Software tools Clustal W, MEGA, MicroSyn, BLASTP, Circos
Organisms Arabidopsis thaliana, Oryza sativa
Chemicals Amino Acids