Format

Send to

Choose Destination
Nucleic Acids Res. 2001 Nov 1;29(21):4395-404.

Strain-specific genes of Helicobacter pylori: distribution, function and dynamics.

Author information

1
Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.

Abstract

Whole-genome clustering of the two available genome sequences of Helicobacter pylori strains 26695 and J99 allows the detection of 110 and 52 strain-specific genes, respectively. This set of strain-specific genes was compared with the sets obtained with other computational approaches of direct genome comparison as well as experimental data from microarray analysis. A considerable number of novel function assignments is possible using database-driven sequence annotation, although the function of the majority of the identified genes remains unknown. Using whole-genome clustering, it is also possible to detect species-specific genes by comparing the two H.pylori strains against the genome sequence of Campylobacter jejuni. It is interesting that the majority of strain-specific genes appear to be species specific. Finally, we introduce a novel approach to gene position analysis by employing measures from directional statistics. We show that although the two strains exhibit differences with respect to strain-specific gene distributions, this is due to the extensive genome rearrangements. If these are taken into account, a common pattern for the genome dynamics of the two Helicobacter strains emerges, suggestive of certain spatial constraints that may act as control mechanisms of gene flux.

PMID:
11691927
PMCID:
PMC60179
DOI:
10.1093/nar/29.21.4395
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center