Computational protocol: Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific

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Protocol publication

[…] Excised DGGE bands were sequenced directly from PCR products which were re-amplified with the primer set used above. Prior to sequencing, the PCR products were analysed by DGGE to confirm the band positions relative to the original sample. Bidirectional sequencing was performed with an automatic sequencer 3730xl (Applied Biosystems, Foster City, CA) after sequencing reaction with a BigDye terminator sequencing kit (Applied Biosystems, Foster City, CA) using 341F and 907R primers. Sequences were aligned to known sequences in the DNA Data Bank of Japan (DDBJ) database using blast (). Phylogenetic relationships were inferred from multiple alignments using CLUSTAL W () and draw the phylogenetic tree by neighbour-joining method with mega 3.1 software (). All sequences were checked by the CHECK_CHIMERA program available through the Ribosomal Database Project (). The nucleotide sequences of DGGE bands have been deposited in the DDBJ nucleotide sequence database under accession numbers from AB307969 to AB308000. […]

Pipeline specifications

Software tools Clustal W, MEGA
Databases DDBJ
Application Phylogenetics
Chemicals Bromodeoxyuridine, Thymidine