Computational protocol: A New Thermophilic Nitrilase from an Antarctic Hyperthermophilic Microorganism

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Protocol publication

[…] Genomic DNA of the isolate was extracted using a phenol–chloroform protocol. The genomic DNA of the isolated microorganism was completely sequenced in Georgia Genomics Facility (GGF, University of Georgia, USA) obtaining from it the complete sequence of the 16S rRNA gene (GenBank, accession number SUB1008503 Pyrococcus_sp_M24D13 KT267175) and the NitM24D13 gene. Related sequences were obtained from GenBank database [National Center for Biotechnology Information (NCBI), Bethesda, MD, USA] PDB, SwissProt, PIR, and PRF using the BLAST search program. The sequences were aligned using multiple sequence alignment software, CLUSTAL W ver. 1.81. A phylogenetic tree was constructed with MEGA 5 software (Tamura et al., ) based on the information of complete 16S rRNA sequences of 13 strains similar to Pyrococcus sp. M24D13, using the method of neighbor-joining (Saitpu and Nei, ) with a bootstrap analysis of 1000 replicates. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics