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Mapping the Deinoccocus radiodurans Proteome in Three Dimensions |
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Accelrys uses high throughput annotation methods incorporating sequence- and structure-based analyses to map the Deinococcus Radiodurans genome.
Abstract
White et al. (Science 286: 1571-1577, 1999)described that they were able to assign function to 52% of the sequences in the Deinococcus radiodurans R1 genome. A method of combining sequence- and structure-based computational technologies in an automated pipeline in order to extract functional assignments for an additional 12 % of this genome and other genomes will be presented. Specific results from processing of the Deinococcus radiodurans R1 sequences will be highlighted that demonstrate how 3D-based methods can be used to extend the level and range of functional annotation through homology.
--------------------------------------------------------------------------------Methods
3187 translated protein sequences for Deinococcus radiodurans were downloaded from www.tigr.org. The sequences were then analyzed using three methods from the GeneAtlasT pipeline. A schematic representation of GeneAtlas is shown below, the three methods used are shown in red i.e.
Sequence similarity search (PSI-BLAST)
SeqFold
High Throughput Homology Modeling
GeneAtlas annotates an additional 13.5% of Deinococcus radiodurans with high confidence (assignments scored 2 or 3).
The false positive rate is relatively high (19.6%) unless filtered using knowledge based on the functionally important features of the template. Incorporation of this information has been implemented in GeneAtlas.
3D methods also increase the level of functional information obtained from traditional bioinformatics methods.
FUll article is available on Click here
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Last Updated ( Saturday, 14 May 2005 )
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