Integr8 and Genome Reviews: integrated views of complete genomes and proteomes

Abstract

Integr8 is a new web portal for exploring the biology of organisms with completely deciphered genomes. For over 190 species, Integr8 provides access to general information, recent publications, and a detailed statistical overview of the genome and proteome of the organism. The preparation of this analysis is supported through Genome Reviews, a new database of bacterial and archaeal DNA sequences in which annotation has been upgraded (compared to the original submission) through the integration of data from many sources, including the EMBL Nucleotide Sequence Database, the UniProt Knowledgebase, InterPro, CluSTr, GOA and HOGENOM. Integr8 also allows the users to customize their own interactive analysis, and to download both customized and prepared datasets for their own use. Integr8 is available at

The type 1 pili regulator gene fimX and pathogenicity island PAI-X as molecular markers of uropathogenic Escherichia coli

“…The coding sequences for fimX, hyxR, hyxA and hyxB were gathered for UTI89 (EMBL coding sequence: ABE05839) and O157 : H7 strain ELD933 (EMBL coding sequence: AAG54651) from the EMBL-EBI Integr8 web portal (Kersey et al, 2005). The resulting sequences were aligned using the CLUSTAL W multiple alignment algorithm (Thompson et al, 1994) in the BioEdit Sequence Alignment Editor (Hall, 1999), using the 'Toggle' feature to translate the coding Percentage G+C is plotted as area under the curve for the entire region (betT through ykgE) using a 100 bp window.…”

The Protein-Binding Potential of C2H2 Zinc Finger Domains

“…Current predictions estimate the number of C2H2 domains at ~10,000 (Letunic et al, 2002), or approximately 3% of the human genome (Kersey et al, 2005;Mackay and Crossley, 1998;Matthews and Sunde, 2002).…”

“…1 Reference (Mulder et al, 2007) 2 Reference (Kersey et al, 2005) 3 Percentage of proteome containing proteins with C2H2 domains (Kersey et al, 2005) …”

Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps

“…Our comparison set consists in all pairwise genome comparisons of strains of the same bacteria (intra-species comparisons) as of Jan 2010: it comprises 346 different genomes from 87 species retrieved from Genome Reviews database [5]. First, we searched for local alignments between genome pairs using YASS with default parameters [11].…”