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For gene prediction accuracy assessment, the "genes that are included in the reference genomes" (further referred to as amino acid annotation file), and the "overlap of the genes with the sequencing reads" were also downloaded.
As for the false positives, it can be seen in Figures21 and22 that many pores can be mistaken for false positives unless smaller pores are included in the reference measurement.
Overall, one might evoke a potentially high false positive rate especially since proteins are included in the reference map which are either identified by only one significant peptide hit or where two or more non-significant peptide scores are summed up to a significant protein score.
The remaining studies are included in the reference list.
Consider the extreme case, where all the haplotypes in the study sample are included in the reference panel.
Highest sensitivity would be achieved by our method when all known complete genomic sequences are included in the reference set.
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Published conference abstracts, numbered patents, and archived code with an assigned DOI may be included in the reference list.
However, in the newer MetaCyc version (v 16.0) these pathways have been included in the reference libraries.
In order to be included in the reference list, the publication date for the earliest patent describing a compound target interaction had to be from the period 1990 onwards.
Species identification is based on the assumption that the ITS2 sequence for this species is included in the reference database.
To further increase the number of species represented, available sequences from GenBank were included in the reference databases.
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