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The paper shows how such a database can be constructed and then used to create a novel product.
For this purpose, the concept of coarse database is introduced, according to which smaller-size versions of an appropriately ordered large database can be constructed.
With the rapidly increasing number of structures deposited in the Protein Data Bank (PDB) (Berman et al. 2000), a desirable target database can be constructed for docking-based IVS.
Based on this theory, a database can be constructed and used to filter future imputations and to avoid false positive associations.
Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools.
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These databases can be constructed through object-oriented language and in the scope of this work.NET based db4o is used.
Different from proteomics, False Discovery Rates (FDR) cannot be estimated as no appropriate decoy databases can be constructed.
To solve this problem, we and others have shown that customized SAP polypeptide databases can be constructed from RNA-Seq data.
A false discovery rate (FDR) used in proteomics is not feasible here for the MS/MS spectral matching as no appropriate decoy metabolite databases can be constructed, therefore the results need to be further manually assessed by the user.
Consequently, while sampling large genomic SNP databases, empirical distributions can be constructed and genes subjected to the local forces, such as selection, as opposed to the genome-wide forces, like demography, which can be identified by the outlier approach [30], including the one used in our study and others (e.g. Voight et al. [19], and Wang et al. [20]).
More experienced users can query the database using SQL statements which can be constructed in a uniform manner.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com