Methods for Evolution Analysis

From MDWiki
Jump to navigationJump to search

The protein that is used in this research is a putative N-type ATP pyrophosphatase from Pyrococcus furiosus. This protein is predicted to be similar to ATP Binding Domain 4. From ‘Target Blast and Symatlas Table’, a BlastP search against the NCBI non-redundant protein database can be conducted for both sequences from Pyrococcus furiosus ATP pyrophosphatase and Macaca mulatta ATP binding domain 4. Sequences with small E value were selected and Fasta format of selected sequences were retrieved. Using these selected sequences, a multiple sequence alignment was conducted by using ClustalX. A phylogenetic tree can be constructed based on the best multiple sequence alignment so that the evolutionary relationship between species can be observed. From the phylogenetic tree, bootstrap was performed with 100 replicates. Thus, bootstrap values which indicate the branch length of the tree can be calculated. N-type ATP pyrophosphatase was also searched by using STRING database which will allow the observation of the occurence of the protein superfamily in other species.