lenA and paralogous genes of the previously sequenced L. interrogans serovars Lai and Copenhageni [48], [49] were identified by BLAST-P analyses of GenBank (http://www.ncbi.nlm.nih.gov/blast) and the Institute for Genomic Research TIGRR) Comprehensive Microbial Resource database (http://tigrblast.tigr.org/cmr-blast).
The data are processed automatically with subsequent manual validation to ensure an accurate microbial resource database.
More than half of the pseudogenes (114) were assigned to the 'hypothetical protein' and 'mobile and extrachromosomal element' categories, based on the Comprehensive Microbial Resource database [ 23].
PANDA is JCVI's internal repository of non-redundant and non-identical protein and nucleotide data built periodically from public databases that include the latest protein sequences (e.g. GenBank (http://www.ncbi.nlm.nih.gov), PDB (http://www.rcsb.org/pdb/Welcome.do), UniProt (http://www.uniprot.org/) and the Comprehensive Microbial Resource database (http://www.tigr.org/CMR)).
BLAST-Extend-Repraze (BER) was used to search TIGR's non-redundant amino acid database (nraa) containing all proteins available from GenBank, PIR, SWISS-PROT, and TIGR's Comprehensive Microbial Resource (CMR) database [72].
This comparison was achieved by sequence analysis using the Comprehensive Microbial Resources (CRM) database from JCVI (http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi), and confirmed by BLAST searches.
a Data from these genomes was used in the phylogenetic profiling studies that identified EpsH. a Data was normalized to results from the Comprehensive Microbial Resource which showed 256 hits from a database size of 1048 MB of DNA.
We obtained genomic sequences from the following sources: the Comprehensive Microbial Resource (http://cmr.tigr.org/) for E. coli, the Saccharomyces Genome Database (ftp://genome-ftp.stanford.edu/) for S. cerevisiae, the Eisen Lab (http://rana.lbl.gov/drosophila/) for D. melanogaster, and Ensembl (http://www.ensembl.org/) for M. musculus.
Analysis of the differentially expressed genes according to the Comprehensive Microbial Resource of the J. Craig Venter Institute (CMR-JCVI) L. monocytogenes EGDe genome database role categories showed that the sakacin P-resistant strains had altered expression of genes belonging to the majority of the role categories (Figure S1 and Table S1).
Its product is currently annotated as 'F1/F0 ATPase, Methanosarcina type, subunit 2' (F1F0_chp_2, TIGR03165, DH Haft, December 4, 2006) in the JCVI's Comprehensive Microbial Resource (Davidsen et al., 2010) and as 'ATPase_F1/F0-cplx_su2_Meth-typ' (IPR017581) in the InterPro database (Hunter et al., 2009), whereas UniProt uniformly annotates these proteins as 'Putative uncharacterized protein'.
To determine the functional nature of the newly verified un-annotated genes, intergenic sequence assemblies were searched using blastx [ 35] against TIGR's in-house comprehensive non-identical amino acid database, which includes all proteins available from GenBank, PIR, Swiss-Prot, and TIGR's Comprehensive Microbial Resource catalogue, the Omniome.
