Computational protocol: Uncovering ancient transcription systems with a novel evolutionary indicator

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Protocol publication

[…] Evolutionary distances (dDR and d) were calculated using the nucleotide sequences of the TBP and TFIIB genes from 34 species (). All sequences were derived from the NCBI database. Multiple nucleotide-sequence alignments of direct repeats were performed as follows. First, a multiple amino-acid-sequence alignment of the core region was generated with the amino-acid-sequence data of the 34 species () by using ClustalW2, and the alignment was manually improved according to the results of BLAST2. Then, the amino-acid sequences of the first and second repeats of TBP and TFIIB were aligned using the amino-acid-sequence alignment of the core region on the basis of the tertiary structural superposition of the first and second repeats of TBP and TFIIB. The tertiary structural superposition was obtained from the DALI software. Then, the nucleotide-sequence alignments were prepared on the basis of the amino-acid-sequence alignments for the first and second repeats of TBP and TFIIB ( and ). Evolutionary distances and Newick formats were calculated by the program MEGA5.05 by using a maximum composite likelihood method with default parameters. Nodes of phylogenetic trees in and were swapped by NJplot according to the dDR value. Phylogenetic trees were drawn by the program Unrooted. The molecular graphics were prepared by PyMOL (http://www.pymol.org). […]

Pipeline specifications

Software tools Clustal W, DALI, MEGA, NJplot, PyMOL
Applications Phylogenetics, Protein structure analysis
Chemicals Nucleotides