Computational protocol: Altered Phenotypes in Saccharomyces cerevisiae by Heterologous Expression of Basidiomycete Moniliophthora perniciosa SOD2 Gene

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Protocol publication

[…] MpSOD2 cDNA was identified from a previously constructed mycelial cDNA library in the pDNR-LIB plasmid using DB SMART Creator cDNA (Creator SMART cDNA Library Construction Kit, Clontech, Palo Alto, CA, USA) that had been derived from primordia and mature basidiomata [] (plate identity: CP02-EC-001-002-C06-UE.F, clone C06). Based on its similarity to known SOD2 genes an open reading frame (ORF) analysis was performed (ORFinder program, Lasergene, Madison, WI, USA) followed by homology search with BLAST [] against sequences in the NCBI database. ClustalW was used for multiple sequence alignment of amino acid sequence [].Phylogenetic analysis was by Neighbor-Joining method [] using program MEGA4 []. The bootstrap consensus tree was inferred from 1000 replicates []. Evolutionary distances were estimated using the Poisson correction method []. We eliminated all positions containing gaps and missing data from the analysis (complete deletion option). There were 93 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4. The sequence CDS was predicted by Augustus Gene Predictor v2.7 (Department of Bioinformatics, University of Göttingen, Göttingen, Alemanha) []. […]

Pipeline specifications

Software tools Clustal W, MEGA, AUGUSTUS
Application Phylogenetics
Organisms Saccharomyces cerevisiae, Moniliophthora perniciosa, Coprinopsis cinerea, Laccaria bicolor
Chemicals Amino Acids, Carbon, Diethylnitrosamine, Hydrogen Peroxide, Paraquat, Lactic Acid