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To ensure that the porcine ESTs matched against protein databases are correct matches to mitochondrial proteins, we performed some validating checks.
This indicates that, provided the gene models retrieved from the databases are correct, some PDZ domains are not conserved enough to be detected by the domain prediction programs used in the present study.
Assuming that most peptides in the various databases are correct, we computed the threshold that would maximize the number of presented peptides from the positive databases, and minimize the number of peptides in a neutral set of 1 000 000 random peptides with the NCBI database amino-acid distribution (http://prowl.rockefeller.edu/aainfo/contents.htm).htm
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More than half of the original gene models annotated in the P. sojae and P. ramorum databases were correct, whilst almost all of the original entries for P. infestans were erroneous.
This also means that the data entered into the database are correct at the time of insertion.
This assumes that the genotypes in the HapMap database are correct.
Also, the predictive values were generally very high indicating a high probability that the registrations in the Obstetric Database are correct.
The results indicated that the sequence present in the S. pombe genome database is correct.
To verify that the resulting database was correct, we ran FastBLAST on the combined set of sequences as well, and we selected top homologs for 2,000 genes using either FastBLAST database.
When evaluating the overall quality of data for the enrolled DD2 patients, it is important to consider whether all data are recorded (no missing data) and whether the information recorded in the database is correct.
Rough figures extracted from the PubMed database were corrected because of their underestimation, due to the fact that PubMed's searches are performed only on title and abstract, making our searches blind to most of the text (full-text).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com