Computational protocol: A PKS/NRPS/FAS Hybrid Gene Cluster from Serratia plymuthica RVH1 Encoding the Biosynthesis of Three Broad Spectrum, Zeamine-Related Antibiotics

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Protocol publication

[…] The selected BAC-clone was subcloned using pUC19 vectors and sequenced by a combination of primer walking and shotgun sequencing. Sequencing reactions were run using Big Dye Terminator mix (Applied Biosystems), purified and analyzed on an ABI 3130 genetic analyzer. Sequence assembly into contigs was performed using Sequencher 4.8 software (Gene Codes Corporation, USA). ORF predictions were carried out by combining comparative genomics approaches (tBLASTx) and the ORF Finder (NCBI) and Genemark.hmm algorithms . […]

Pipeline specifications

Software tools Sequencher, TBLASTX, Open Reading Frame Finder, GeneMark.hmm
Applications Genome annotation, Phylogenetics, Nucleotide sequence alignment
Organisms Serratia plymuthica, Bacteria, Escherichia coli
Chemicals Fatty Acids, Unsaturated