Computational protocol: PCR-based detection of composite transposons and translocatable units from oral metagenomic DNA

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[…] The analysis of sequencing results was performed with BioEdit software version 7.2.0 (http://www.mbio.ncsu.edu/bioedit/bioedit.html). If the insert was sequenced using multiple primers, the sequences were assembled with CAP contig function within the software (Huang ). The vector sequences were initially trimmed from the sequences by using VecScreen analysis tool (http://www.ncbi.nlm.nih.gov/tools/vecscreen) and identified for the primer binding sites. The sequences were then analyzed by using BlastN and BlastX for the matching with the sequences in the databases, ISFinder for the identification of IS element and Clustal Omega for the alignment of the sequences (Altschul et al.; Siguier et al.). The sequences of all composite transposons (CTA1 to CTA5) were submitted to the DNA database with the accession numbers from KX305930 to KX305934. […]

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