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9mer Peptide Distribution Derived from 169 HIV-1 Subtype B Gag and Nef Protein Sequences

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posted on 21.02.2013, 12:36 by David C Nickle, Morgane Rolland, Mark A Jensen, Sergei L. Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I Mullins, Nebojsa Jojic

Each bin in the histogram represents the number of 9mers from a particular frequency class plotted on a log scale. There are only a few peptides found at high frequencies, whereas most of the 9mers occur only once or twice. The score of a given frame is the sum of the frequencies of each unique 9mer contained by the frame. The possible extreme value frequencies for each peptide from all rare to all common is 1.198 × 10−5 − 0.0020 for Gag (black bars) and 2.988 × 10−5 − 0.0051 for Nef (gray bars). The differences in the two distributions can be explained by the differences in gene length and levels of conservation.


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