Computational protocol: Molecular characterisation of the STRUBBELIG-RECEPTOR FAMILY of genes encoding putative leucine-rich repeat receptor-like kinases in Arabidopsis thaliana

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Protocol publication

[…] Homology searches were done with the BLAST tool []. The signal peptide sequences, the proline-rich regions, the transmembrane domains, and the PEST motifs were determined using the SMART [], PROSITE [], PSORT [], and PESTfind [] websites. The kinase domains were detected through the PlantsP database []. The subdomain organisation of the kinase domains was inferred from published kinase alignments []. Sequence alignments were done with MultAlin [,] using the following parameters: symbol comparison table: identity, gap weight: 5, gap length weight: 0, consensus levels: high = 100% low = 60%. Phylogenetic tree analysis of the SRF family was performed using an amino acid sequence alignment generated by the program DAMBE [] using a gap penalty value of 20. Using this alignment a maximum likelihood tree was generated in TREE-PUZZLE [] with the help of the JTT model of substitution. Rate heterogeneity was estimated with the gamma distribution model with eight rate categories as described in []. We also tested different approaches (Baysian inference, Neighbor-joining) but the topology of the tree did not change. TREEVIEW was used to visualise the tree []. [...] Pictures of plants or various plant organs were taken with an SZX12 stereo microscope from Olympus coupled to a ColorView III digital camera and using Cell^P software (Olympus Europa GmbH, Hamburg, Germany). Images were saved as TIFF files and adjusted for color and contrast using Adobe Photoshop CS2 (Adobe, San Jose, CA, USA) software on an iMac G5 computer (Apple, Cupertino, CA, USA). Composites were also generated by Adobe Photoshop CS2. Line drawings were generated using Adobe Illustrator CS2. […]

Pipeline specifications

Software tools PSORT, MultAlin, DAMBE, TREE-PUZZLE, TreeViewX, Adobe Illustrator
Databases PROSITE PlantsP
Applications Miscellaneous, Phylogenetics, Protein sequence analysis
Organisms Arabidopsis thaliana