13,981 research outputs found
GenomeFingerprinter and universal genome fingerprint analysis for systematic comparative genomics
How to compare whole genome sequences at large scale has not been achieved
via conventional methods based on pair-wisely base-to-base comparison;
nevertheless, no attention was paid to handle in-one-sitting a number of
genomes crossing genetic category (chromosome, plasmid, and phage) with farther
divergences (much less or no homologous) over large size ranges (from Kbp to
Mbp). We created a new method, GenomeFingerprinter, to unambiguously produce
three-dimensional coordinates from a sequence, followed by one
three-dimensional plot and six two-dimensional trajectory projections to
illustrate whole genome fingerprints. We further developed a set of concepts
and tools and thereby established a new method, universal genome fingerprint
analysis. We demonstrated their applications through case studies on over a
hundred of genome sequences. Particularly, we defined the total genetic
component configuration (TGCC) (i.e., chromosome, plasmid, and phage) for
describing a strain as a system, and the universal genome fingerprint map
(UGFM) of TGCC for differentiating a strain as a universal system, as well as
the systematic comparative genomics (SCG) for comparing in-one-sitting a number
of genomes crossing genetic category in diverse strains. By using UGFM,
UGFM-TGCC, and UGFM-TGCC-SCG, we compared a number of genome sequences with
farther divergences (chromosome, plasmid, and phage; bacterium, archaeal
bacterium, and virus) over large size ranges (6Kbp~5Mbp), giving new insights
into critical problematic issues in microbial genomics in the post-genomic era.
This paper provided a new method for rapidly computing, geometrically
visualizing, and intuitively comparing genome sequences at fingerprint level,
and hence established a new method of universal genome fingerprint analysis for
systematic comparative genomics.Comment: 63 pages, 15 figures, 5 table
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
The organization and mining of malaria genomic and post-genomic data is
highly motivated by the necessity to predict and characterize new biological
targets and new drugs. Biological targets are sought in a biological space
designed from the genomic data from Plasmodium falciparum, but using also the
millions of genomic data from other species. Drug candidates are sought in a
chemical space containing the millions of small molecules stored in public and
private chemolibraries. Data management should therefore be as reliable and
versatile as possible. In this context, we examined five aspects of the
organization and mining of malaria genomic and post-genomic data: 1) the
comparison of protein sequences including compositionally atypical malaria
sequences, 2) the high throughput reconstruction of molecular phylogenies, 3)
the representation of biological processes particularly metabolic pathways, 4)
the versatile methods to integrate genomic data, biological representations and
functional profiling obtained from X-omic experiments after drug treatments and
5) the determination and prediction of protein structures and their molecular
docking with drug candidate structures. Progresses toward a grid-enabled
chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system
We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license
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