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Conserved domain identification and phylogenetic analysis

PG Pingan Guo
YZ Yancheng Zheng
DP Dingxiang Peng
LL Lijun Liu
LD Lunjin Dai
CC Cong Chen
BW Bo Wang
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The T-Coffee program was used to perform a multiple sequence alignment of the PP2 proteins from different species (http://www.ebi.ac.uk/Tools/msa/tcoffee/)45, and then we used Web-Logo (http://weblogo.berkeley.edu/logo.cgi) to represent the results46. The amino acid sequences were analyzed using the Conserved Domain Architecture Retrieval Tool (CDART)47. The multiple alignments of BnPP2 proteins were analyzed by the MAFFT algorithm48. Phylogenetic trees were constructed in MEGA 6.0 software with the default settings by using the maximum likelihood method with 1000 bootstrap replications49.

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