Here a step-by-step protocol is presented in sufficient detail to allow a novice to start with a sequence of interest and to build a publication-quality tree illustrating the evolution of an appropriate set of homologs of that sequence. Finally, MEGA provides a powerful and flexible interface for the final step, actually drawing the tree for publication. Here we illustrate the maximum likelihood method, beginning with MEGA's Models feature, which permits selecting the most suitable substitution model. For the third step, construction of a phylogenetic tree from the aligned sequences, MEGA offers many different methods. For the second step, alignment of those sequences, MEGA offers two different algorithms: ClustalW and MUSCLE. The first step, identification of a set of homologous sequences and downloading those sequences, is implemented by MEGA's own browser built on top of the Google Chrome toolkit. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. In the example illustrated here, the program MEGA is used to implement all those steps, thereby eliminating the need to learn several programs, and to deal with multiple file formats from one step to another (Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. This Protocol describes the several steps required to produce a phylogenetic tree from molecular data for novices. In fact, it is a fairly straightforward process that can be learned quickly and applied effectively. Phylogenetic analysis is sometimes regarded as being an intimidating, complex process that requires expertise and years of experience. The developed model predicted strong binding affinity for Tyr 47. In addition, the three dimensional structure of capsicein was modelled, and the binding affinity of sterol and capsicein was studied using molecular docking. Further sequence analysis identified promoter sequence, transcription start site, a leader signal sequence and a core elicitin domain, with a conserved 6 Cysteine residues. Local BLAST search against full genome identified entire coding sequence. capsici, by querying the amplified product against the genome. Subsequently, attempt was made to characterize the complete gene of elicitin from genome sequence information of P. The PCR amplified product size of 256 bp length and the BLAST analysis of the sequenced product showed perfect match with alpha-elicitin sequences of P. Elicitin sequence was amplified using primers designed from the known Elicitin genes of other Phytophthora organisms based on their conserved motifs. capsici, an Oomycete plant pathogen which causes significant damage to a broad range of host plants. Here, we report the cloning of Elicitin gene from P. Elicitins are a family of small proteins secreted by Phytophthora, which induce leaf necrosis in infected plants.
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