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[…] b'd. Only the primary transcript was chosen when alternative transcripts occurred. In addition, five partial SDH protein sequences of P. bretschneideri [] and one SDH sequence of Eriobotrya japonica [] were obtained from literature searches. Homologous SDHs of P. hortorum were provided by the P. hortorum genome sequencing project author (Prof. Robert K. Jansen, The University of Texas at Austin)., The Uniprot database was queried for previously identified MDR mammal SDHs and yeast SDHs. Only reviewed entries were selected and used as the out-group in this phylogenetic analysis. Multiple sequence alignments of 102 sequences (92 plant SDHs, 7 mammal SDHs and 3 yeast SDHs) were carried out using ClustalW2 []. The evolutionary distances of target SDHs (pairwise p-distance) were estimated using MEGA6 software []. The Neighbour Joining tree was inferred by MEGA6 software [] using the p-distance [] substitution model, the certainty at each node was assessed by the Interior-branch Test method (1000 times iteration). Maximum likelihood trees were estimated by MEGA6 software [] using the JTT+GAMMA substitution model [], the best fitting model as determined by the \xe2\x80\x9cFind Best DNA/Protein Models\xe2\x80\x9d function in MEGA6. Bootstrap supports for Maximum likelihood trees were calculated from 1000 replicates. For both Neighbour Joining and Maximum likelihood methods, the Gaps/Missing Data Treatment parameter was set as Complete-Deletion to eliminate the effects of gaps and insertions. The developed phylogenetic trees were rooted on the yeast SDHs and annotated using the FigTree version 1.4.2 software (http://tree.bio.ed.ac.uk/software/figtree/)., Preliminary sequence identity of SDHs was obtained by local all-vs-all BLAST using NCBI-BLAST-2.2.29 tool [] downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/. The BLAST results were sorted according to respective phylogeny groups. Average pair-wise sequence identities were calculated using Microsoft Excel software based on the BLAST results. Protein functional domains were predicted using InterPro (http://www.ebi.ac.uk/interpro/). Secondary structure analysis was implemented with ESPript3.0 tool (http://espript.ibcp.fr/ESPript/ESPript/) using human SDH (PDB: 1PL8) as a template. All resid' […]

Pipeline specifications

Software tools Clustal W, MEGA, FigTree, InterPro