Normalization strategy and sorting of PHASTpep.

Abstract

<p>(A) For each screen, the frequencies were divided by the total number of reads of the screen, followed by the frequency of that sequence in the reference library. (B) In order to demonstrate the sorting process, small libraries were created that represented a reference library, two positive screens, and 2 negative screens. For each sequence, a qualitative ranking was determined (predicted ranking) based on the level of frequency assigned in each library. For example, GVTHKLQ was absent in the reference library, high in both positive screens, and absent in both negative screens. Therefore, it was predicted to be ranked very high. Conversely, TPSIYFL was only high in the negative screens and absent elsewhere. Thus it was predicted to rank very low. For each test case (sequence), the predicted ranking was compared to the actual ranking after running the test libraries through our sorting software. R, reference; PS, positive screen; NS, negative screen; A, absent; L, low; H, high.</p