Pipeline publication

[…] the Dof factors in Chinese cabbage. Our study will support recourses for understanding how BraDof transcription factors respond to abiotic stresses and the interaction of these genes for abiotic stress response mechanism., The nucleotide and protein sequences of BraDof factors from B. rapa L. ssp. pekinensis were collected from the BRAD (http://brassicadb.org/brad/) database []. We used the BLAST program available on the NCBI (National Center for Biotechnology Information) database to search for potential Dof domains (http://www.ncbi.nlm.nih.gov/). The sequences of all Dof transcription factors in other species were downloaded from the plant TFDB database (http://planttfdb.cbi.edu.cn/) []., MEME Suite was used to identify all motifs in the BraDof protein sequences []. Analysis was performed using the following parameters: number of repetitions, if any; optimum width of the motif, 6–50; and maximum number of motifs, 15. Identified BraDof domains were aligned using 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 [,]., Several physiological and biochemical indices were also analyzed. The theoretical pI was calculated by ExPASy (http://web.expasy.org/compute_pi/) []. 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) []. The synteny of the BraDof genes was calculated by MicroSyn software according to Cai’s means (http://fcsb.njau.edu.cn/microsyn/) []., OrthoMCL was used to search for orthologous and paralogous genes in Chinese cabbage, Arabidopsis, and rice using the entire Dof protein sequences []. 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/) []. 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 Laborat […]

Pipeline specifications

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