Similar protocols

Protocol publication

[…] les with a 260/280 nm absorbance ratio of 1.8–2.0 and a 260/230 nm absorbance ratio of 2.0–2.2 were considered pure and then used for the library construction and sequencing., 2-KGA and different substrates were detected by HPLC using an Aminex HPX-87H column (Bio-Rad, Hercules, CA, USA) coupled with a refractive index (RI) detector. 5 mM H2SO4 was used as the mobile phase at a speed of 0.6 mL/min and the RI temperature was kept at 65 °C., Using the 454 GS FLX system, single-end libraries with 15-fold coverage and mate paired-end libraries with 10-fold coverage were constructed. The genome was sequenced by the Sanger shotgun approach. The reads were assembled into 6 contigs by using the 454 Newbler assembler and the gaps between the contigs were closed by PCR amplification., The genome analysis was carried out by the Rapid Annotation using Subsystems Technology (RAST) analysis platform. The function of genes was also annotated by using BLAST against Kyoto Encyclopedia of Genes and Genomes (KEGG) database and Clusters of Orthologous Groups of proteins (COG) database. The tRNAs and rRNAs were predicted by tRNAscan-SE and RNAmmer. The subcellular location of proteins and the signal peptides were predicted by PSORT and SignalP 4.0. The origin of replication (oriC) and putative DnaA boxes were identified by Ori-Finder. CVTree was performed for the phylogenetic analysis and the phylogenetic tree was generated using the MEGA program. The GC-Profile was used to compute the GC content variation in DNA sequences and to predict the horizontal gene transfer. CGView Server was used for the visualization of circular genomes and the metabolic network was constructed by KEGG automatic annotation server KAAS., The sequence of the K. vulgare Hbe602 genome has been deposited at DDBJ/EMBL/GenBank under the accession numbers C […]

Pipeline specifications

Software tools Newbler, RAST, tRNAscan-SE, RNAmmer