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Pipeline publication

[…] re was grown overnight on plate count agar (Difco, UK) at 28 °C. Genomic DNA was isolated using the PureLink™ Genomic DNA Mini Kit (Invitrogen, USA) according to the manufacturer’s instructions., The genomic DNA of P. alcaliphila JAB1 was used to prepare shotgun and 8 kb paired-end 454 sequencing libraries according to the Library Preparation Method Manual (Roche). These libraries were sequenced with the GS FLX instrument using GS FLX+ chemistry (Roche) at the Institute of Molecular Genetics AS CR (Prague, Czech Republic). The resulting 110,702 shotgun and 461,976 paired-end reads comprised a total of 221,447,771 bases and represented 41.5-fold genome coverage. These reads were assembled in Newbler 2.8 software (Roche), and gaps were closed by local assembly of selected reads in Staden software [] into a single circular contig., The NCBI Prokaryotic Genome Annotation Pipeline [] was used for automated genome annotation, and functional annotations were carried out by searching against KEGG [], COG [] and Pfam [] databases. SignalP [] and TMHMM [] tools were used for the prediction of genes with signal peptides and transmembrane helices, respectively. Searches against NCBI-NR [], RefSeq [], UniProtKB/Swiss-prot [] and TCDB [] were carried out for functional assignment of selected genes., The P. alcaliphila JAB1 genome consists of a single 5,340,293 bp-long chromosome with a GC content of 62.5% (Fig. ). The 4908 predicted genes correspond to an 89% coding density. The genome contains 4773 CDS, 65 tRNA genes for all 20 amino acids, 4 rRNA operons, 4 ncRNA genes, 3 CRISPR repeats and 54 pseudogenes. Function was assigned to 3816 CDS, with 957 CDS annotated as hypothetical proteins only (Table ). The distribution of COG functiona […]

Pipeline specifications

Software tools Newbler, Staden, PGAP, SignalP, TMHMM
Databases UniProtKB