Computational protocol: Characterization of a Novel Serine Protease Inhibitor Gene from a Marine Metagenome

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[…] DNA sequence analysis was performed using the BigDye Terminator Cycle sequencing kit on an ABI Prism 3700 DNA analyzer (Applied Biosystems, USA). Protein translation was carried out using the web-based translation tool at the ExPaSy homepage []. Sequence predictions were retrieved from the protein and nucleotide databases at NCBI Entrez page []. Sequence similarity searches were performed with the BLAST 2.0 program. The amino acid sequence alignment of Spi1C with homologous proteins was done using the AlignX program, a component of the Vector NT1 suite (InforMax, North Bethesda, MD, USA) using the blosum62mt2 scoring matrix. Based on the comparison of the deduced amino acids, a putative gene (Spi1C) encoding a novel serpin was identified and further characterized. A phylogenetic tree was constructed using the neighbor-joining method with MEGA 4.0 software []. Boot-strapping values were used to estimate the reliability of the phylogenetic reconstructions (1000 replicates). […]

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