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We have therefore developed functionality that transforms annotated bacterial genomes present at the NCBI genome repository into so called GenomeMaps.
Currently there are 1,390 complete genomes [ 1] annotated in the KEGG genome repository and many more are in progress.
Complete and published genome sequences of 211 anaerobic bacteria (Additional file 1: Table S1) were obtained from the NCBI Refseq and draft genome repository.
b Genome sequence found: complete or incomplete in the pig genome assembly, found in the Traces archive, or Not Found in any genome repository.
Synechocystis sp. PCC6803 genome and annotation files were downloaded from NCBI Entrez Genome repository as of date 10 of September of 2008 [ 51].
Addition of this species to the genome repository will provide an excellent resource for studying the genetic basis of limb loss and trunk elongation.
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A major goal during the development of the MGP Portal was to create a reproducible workflow for the creation of well-annotated and visually accessible genome repositories.
The gene set enrichment and the pathway analysis were only taught for Affymetrix microarrays by using the available Kyoto Encyclopedia for Genes and Genomes repository (Kanehisa and Goto, 2000).
Thus, each COG (listed in Table 1) was used as a bait to retrieve potential T6SS encoding regions from the 506 complete genomic sequences of the Genome Reviews Repository (September 2007, see Materials and methods §1).
The data sets supporting the results of this article are available in the EmbryoGENE genome browser repository, http://www.emb-bioinfo.fsaa.ulaval.ca/DeMontera2012/ //www.emb-bioinfo.fsaa.ulaval.ca/DeMontera2012/
Genomic sequences available as of July 15 , 2013 for the entries Klebsiella, K. pneumoniae, and K. variicola, were downloaded from the NCBI National Center for Biotechnology Informationn) genome sequence repository (http://www.ncbi.nlm.nih.gov/genome/).nih.gov/genome/
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