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

Kersey, Paul J.; Bower, Lawrence; Morris, Lorna; Horne, Alan; Petryszak, Robert; Kanz, Carola; Kanapin, Alexander; Das, Ujjwal; Michoud, Karine; Phan, Isabelle; Gattiker, Alexandre; Kulikova, Tamara; Faruque, Nadeem; Duggan, Karyn; McLaren, P.G.; Reimholz, B; Duret, Laurent; Penel, Simon; Reuter, Ingmar; Apweiler, Rolf

doi:10.1093/nar/gki039

Cited by 135 publications

(131 citation statements)

References 32 publications

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“…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.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2013

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Uropathogenic Escherichia coli (UPEC) fall within a larger group of isolates producing extraintestinal disease. UPEC express type 1 pili as a critical virulence determinant mediating adherence to and invasion into urinary tract tissues. Type 1 pili expression is under regulation by a family of site-specific recombinases, including FimX, which is encoded from a genomic island called PAI-X for pathogenicity island of FimX. Using a new multiplex PCR, fimX and the additional PAI-X genes were found to be highly associated with UPEC (144/173583.2 %), and more prevalent in UPEC of lower urinary tract origin (105/120587.5 %) than upper urinary tract origin (39/53574 %; P,0.05) or commensal isolates (28/78536 %; P¡0.0001). The Fim-like recombinase gene fimX is the only family member that has a significant association with UPEC compared to commensal isolates. Our results indicate PAI-X genes, including the type 1 pili regulator gene fimX, are highly prevalent among UPEC isolates and have a strong positive correlation with genomic virulence factors, suggesting a potential role for PAI-X in the extraintestinal pathogenic E. coli lifestyle.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2013

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“…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).…”

Section: C2h2 Zinc Finger Domainmentioning

confidence: 99%

“…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) …”

Section: C2h2 Zinc Finger Domainmentioning

confidence: 99%

The Protein-Binding Potential of C2H2 Zinc Finger Domains

Brayer

Kulshreshtha

Segal

2008

Cell Biochem Biophys

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“…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].…”

Section: Resultsmentioning

confidence: 99%

Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps

Mancheron

Rivals

2010

Comparative Genomics

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Abstract. Chaining fragments is a crucial step in genome alignment. Existing chaining algorithms compute a maximum weighted chain with no overlaps allowed between adjacent fragments. In practice, using local alignments as fragments, instead of MEMs, generates frequent overlaps between fragments, due to combinatorial reasons and biological factors, i.e. variable tandem repeat structures that differ in number of copies between genomic sequences. In this paper, in order to raise this limitation, we formulate a novel definition of a chain, allowing overlaps proportional to the fragments lengths, and exhibit an efficient algorithm for computing such a maximum weighted chain. We tested our algorithm on a dataset composed of 694 genome couples and accounted for significant improvements in terms of coverage, while keeping the running times below reasonable limits.

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

Cited by 135 publications

References 32 publications

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

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

The Protein-Binding Potential of C2H2 Zinc Finger Domains

Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps

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