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Genealogy Web sites can be broad-based, with extensive databases, or very small, with more specific databases.
However, more specific databases that are focused only on gene promoters, such as The Eukaryotic Promoter Database (EPD) or Cold Spring Harbor Laboratory mammalian promoter database (CSHLmpd), are also available [8], [9].
The protein engineering and evolution research for these target proteins basing either on naïve error-prone or on direct mutagenesis with more specific databases and tools, such as 3DM (Kourist et al. 2010), have also been planned for our future research.
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Combining this more accurate and more specific database with a more selective querying approach provided the highest true positive and the lowest false positive identification rate among all the databases and their querying algorithms tested.
Certainly, the correlations would become more relevant with a more specific expression database (e.g., amygdala), and cases can be conjectured for which our approach would be uninterpretable (e.g., G × E QTLs using only baseline gene expression databases).
While these generalized databases are valuable resources, more phyla-specific databases are also being developed to address the needs of specific research communities, including providing additional resources not available from the more generalized bacterial databases.
In a companion paper (Brown et al. 2015), the latest modifications to the general structure of the GEOMAGIA50 database and more specific changes to the archeo/volcanic database are described.
On the other hand, advance or complex search is more computationally rich wherein users can filter or restrict the search terms and run multiple queries at a time to get more specific information from the database.
Compared with analysis based on anomalies in the DFD (dinucleotide frequency distribution), which have little specificity, analysis using RepeatMasker is much more specific because it uses a database (RepBase) of consensus sequences from the principal characterized transposable elements.
Low expected E-values result for searches using the option of our tardigrade specific databases: a more specific smaller database reduces the probability of false positives.
Comparison with reference (nucleotide or amino acid general databases) or more specific collections, such as those from genomes, gene families, transcriptomes, or repeats, is fundamental to transfer information from already annotated molecules to newly defined ones.
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