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This eliminates over 95% of the starting database from further consideration.
This notwithstanding, in fact, the realization of the physical project should be addressed by a starting database, also invaluable in order to test its effectiveness.
The relative increase between the starting metabolite set and the resulting MINE is dependent on the specific compounds present in the starting database.
Typically we have seen the ability to eliminate well over 90% of the decoy molecules in the starting database while retaining about 80% of the true positives.
This could probably be explained considering the higher chemical diversity present among the carboxylic acids, which were higher in number compared to the tetrazoles and sulfonamides in the starting database.
These curated sequences were fed back into the starting database and the BLAST and clustering analyses were re-performed to ensure that spurious results had not been generated by incorrect sequences.
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It feeds the input sequences through a pipeline of sequence comparisons against various databases starting with rRNA databases (using BLASTN) followed by mitochondrial protein databases (using BLASTX) and other protein databases.
Irrespective of the starting material database, we obtained a good agreement between average of medicinal and computational chemist scores for the ensemble of compounds; as well as between all chemists and SYLVIA SA scores with a correlation of 0.7.
atBioNet provides several options for network analysis, such as the choice of the starting PPI database, control of the stringency of node additions during network construction, etc.
"He should just dump the database business," says Michael Stonebraker, who started two database firms before founding yet another software venture, Cohera.
Before we started our database application effort, data were scattered in different formats, no database was available and results were calculated by in-house software using Excel macros or resorting to more limited academic or commercial solutions.
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