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In all cases, one unique match was identified.
The simplest interpretation of the CGH data are that many Down structural variants are DownPAV, given that the CGH platform was purposefully designed with probes that have one unique match (one copy) in the "Williams 82" reference genome sequence.
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Each identified protein required at least one unique peptide match.
Only reads with one unique best match in the reference genome and ≤ 2 mismatches every 36 bp, and ≤ 3 bp tails were used for subsequent analyses.
The database search resulted in 127 proteins and most of these were identified at the minimal confidence level, which was only one unique peptide sequence matched.
In this study, more than one hundred proteins were identified and most of these were identified at the minimal confidence level, which was only one unique peptide sequence matched.
The most common corresponded to multiple oligonucleotides matching one unique gene product sequence.
Of which, 101 RAD tags produced a unique match to one scaffold (e ≤ 1.0-20; see File S4).
Thus, to consider a protein identified in this study, we required it to have been matched by at least two peptides, at least one of which was a unique match to a single region in the genome.
We physically mapped the oligonucleotides to the most up-to-date version of the genome assembly [ 48] with the threshold that each oligonucleotide must match to one unique gene with 90% or higher sequence identity.
As expected, Table 3 illustrates that the best results are achieved with partial matches and one unique PHI category (95% precision, 78% recall and 67% F2-measure), decreasing dramatically when considering fully-contained matches (58% precision, 36% recall, 37% F2-measure).
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