Computational protocol: Specialized Hydrocarbonoclastic Bacteria Prevailing in Seawater around a Port in the Strait of Malacca

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Protocol publication

[…] Tag and primer regions used for PCR were removed from the sequences by using QIIME (http://www.qiime.org/; ) through OTUMAMi (http://www.mwm.k.u-tokyo.ac.jp:8080/Plone?set_language=en) and manually with a sequence editing software Se-Al (http://tree.bio.ed.ac.uk/software/seal/) after alignment of sequences using ClustalX (version 2.1; ). The sequences were then checked for putative chimera sequences using Bellerophon server and Mallard program after aligned with the ClustalX. Sequences indicated to be chimera by the both programs were removed, and then the sequences were used for the bacterial community composition analysis in this study. The sequences used were deposited in DDBJ Sequence Read Archive (DRA) under accession numbers DRZ000062 and DRZ000063.Ribosomal Database Project (RDP; ) was used for classifying the sequences into phylum/class, clustering the sequences into operational taxonomic units (OTUs), selecting representative sequences from each OTU, and calculating Chao 1 richness estimates , . The representative sequences were compared to DNA sequences in the GenBank database by using BLAST . […]

Pipeline specifications

Software tools QIIME, Se-Al, Clustal W
Application Nucleotide sequence alignment
Organisms Escherichia coli, Bacteria
Chemicals Carbon, Hydrocarbons