Computational protocol: Isolation, Screening and Identification of Swine Gut Microbiota with Ochratoxin A Biodegradation Ability

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Protocol publication

[…] The 16S rDNA sequence was determined by cycle sequencing. All reference sequences were obtained from GenBank database in NCBI (http://blast.ncbi.nlm.nih.gov/Blast) Sequences were aligned using a multiple sequence alignment tool (ClustalX (1.8). A total of 20 sequences were obtained from NCBI BLAST searches, and were used together with the MM11 sequence to generate a phylogenetic tree. The sequences were aligned manually using Se-Al v. 2.0a11 alignment software (). The aligned sequences were exported in NEXUS format. Phylogenetic trees were inferred from the optimized alignment by distance analysis using PAUP 4.04a software. Eubacterium biforme was used as the outgroup for all analysis. Distance and branching order was performed using the neighbor joining method (). […]

Pipeline specifications

Software tools Clustal W, BLASTN, Se-Al, PAUP*
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Sus scrofa, Zea mays subsp. mays