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Sökning: WFRF:(Sicheritz Ponten Thomas) > (2000-2004)

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  • Jensen, Lars Juhl, et al. (författare)
  • Analysis of two large functionally uncharacterized regions in theMethanopyrus kandleri AV19 genome
  • 2003
  • Ingår i: BMC Genomics. - 1471-2164 .- 1471-2164. ; 4, s. 12-
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: For most sequenced prokaryotic genomes, about a third of the protein coding genes annotated are "orphan proteins", that is, they lack homology to known proteins. These hypothetical genes are typically short and randomly scattered throughout the genome. This trend is seen for most of the bacterial and archaeal genomes published to date. RESULTS: In contrast we have found that a large fraction of the genes coding for such orphan proteins in the Methanopyrus kandleri AV19 genome occur within two large regions. These genes have no known homologs except from other M. kandleri genes. However, analysis of their lengths, codon usage, and Ribosomal Binding Site (RBS) sequences shows that they are most likely true protein coding genes and not random open reading frames.CONCLUSIONS: Although these regions can be considered as candidates for massive lateral gene transfer, our bioinformatics analysis suggests that this is not the case. We predict many of the organism specific proteins to be transmembrane and belong to protein families that are non-randomly distributed between the regions. Consistent with this, we suggest that the two regions are most likely unrelated, and that they may be integrated plasmids.
  • Knudsen, Steen, et al. (författare)
  • GenePublisher : automated analysis of DNA microarray data
  • 2003
  • Ingår i: Nucleic Acids Research. - 0305-1048 .- 1362-4962. ; 31:13, s. 3471-3476
  • Tidskriftsartikel (refereegranskat)abstract
    • GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with a specification of the data. The server performs normalization, statistical analysis and visualization of the data. The results are run against databases of signal transduction pathways, metabolic pathways and promoter sequences in order to extract more information. The results of the entire analysis are summarized in report form and returned to the user.
  • Sicheritz-Pontén, Thomas (författare)
  • Bioinformatic tools for the analysis of microbial genomes
  • 2000
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • High throughput genome sequencing projects are producing an enormous amount of rawdata which has to be converted into biological knowledge. The newly established field ofbioinformatics is concerned with the continuous development of novel methods and toolsfor the comparative analysis of DNA sequences and genomic data.The primary task of bioinformatics in genome sequencing projects is to identify andfunctionally classify all proteins putatively encoded by the genome. Due to the amountof data, first time analyses in large-scale projects have to be rudimentary and fast. We have sequenced Rickettsia prowazekii, an α-proteobacterium and the cauative agent of epidemic typhus in humans. For the analysis of the R. prowazekii genome we have developed CapDB, a sequence analysis and management system for automatic functional gene annotations and graphical display of the genome together with the biological information.Analysis of the 1.111.523 bp R. prowazekii genome revealed 834 complete open read-ing frames of which 523 could be linked to a biological function. In addition, 12 putativepseudogenes and an unusually high proportion of non-coding DNA (24%) were identified.Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondriathan other microbes studied thus far.With the availability of complete genomes, new ways of comparing organisms haveemerged., To study genomic structures, we have developed tools and methods for geneorder based comparisons (GRS) and complete genome alignments (GOBLIN). We de-fine the complete set of phylogenetic trees derived from the proteome of an organism asthe "phylome" and present software for automatic, large-scale reconstructions of phylo-genetic relationships - thus setting the stage for phylogenomic comparisons of microbialgenomes which are likely to reveal a rich web of evolutionary connections.
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