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Computational and Mathematical Methods in Medicine
Volume 2013, Article ID 491612, 13 pages
Research Article

Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2

Received 6 May 2013; Accepted 30 July 2013

Academic Editor: Yanxin Huang

Copyright © 2013 Wadim L. Matochko and Ratmir Derda. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Figure S1. Testing the performance of random indexing function.

Scheme S1. Matlab scripts of random indexing functions and scripts used to generate figure S1.

Scheme S2. Implementation of sampling operator acting on Fre vector.

Scheme S3. Implementation of the operator that calculates confidence interval; scripts has rudimentary error check features and progress display (waitbar).

Figure S2. Estimation of the total solutions for the Sa(M) operator, where M is a multiset, using rate of convergence.

Figure S3. Properties of the Sa(M) solutions for multisets that have elements with very different copy numbers.

Figure S4. Visualization of the Sa(M) solutions for sparse multiset with [1 2 4 8 16 32 64] frequency vector on linear and log scale.

Figure S5. Distribution of errors in censored reads.

Table S1. Top 30 sequences censored during the 13n → 30n process.

Table S2. Top 30 sequences censored during the 1n → 13n process.

  1. Supplementary Materials