From: Optimized design and assessment of whole genome tiling arrays

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From: Optimized design and assessment of whole genome tiling arrays Fig. 1. Design strategy. (A) The genomic sequence is subdivided in unit-sized windows. Within each window, all minimum unique substrings with length ≤K are determined. These are the basis for the uniqueness scoring to design optimized probes. (B) Uniqueness scoring function (exemplified by Mus musculus, chr17:3028401-3028500). The shown sequences represent all the minimum unique prefixes for a unit window. In each window of seed length h, the uniqueness score is calculated by counting the number of minimum unique substrings. For the windows shown, the uniqueness scores are 7, 9, 7, 4, 1, 0. The minimum unique substrings that add to the score are indicated by stars. From: Optimized design and assessment of whole genome tiling arrays Bioinformatics. 2007;23(13):i195-i204. doi:10.1093/bioinformatics/btm200 Bioinformatics | © 2007 The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

From: Optimized design and assessment of whole genome tiling arrays Fig. 4. Density plots of optimized characteristics for our high-coverage and high-uniqueness tiling array designs and comparison to commercial whole-genome tiling arrays. (A) The full design uniqueness score per base, Tm distribution and the uniqueness score per base for the disjoint subsets represented by the non-repetitive and repetitive portions of the mouse genome for our high-coverage U > 0 design containing 19 343 498 probes in the entire design of which 10 565 728 probes are in regions not identified as repetitive and 8 777 770 probes are in repetitive regions; (B) The full design uniqueness score per base, Tm distribution and the uniqueness score per base for the disjoint subsets represented by the non-repetitive and repetitive portions of the mouse genome for our high-uniqueness U > 15 design containing 15 658 735 probes in the entire design of which 10 213 493 probes are in regions not identified as repetitive and 5 445 242 probes are in repetitive regions; (C) The full design uniqueness score per base and the Tm distribution for the NimbleGen 50mers in 100 bp windows whole-genome design containing 14 579 139 probes designed to the non-repetitive portion of the genome and (D) The full design uniqueness score per base and the Tm distribution for the Affymetrix 25mers in 35 bp windows whole-genome design containing 38 346 501 probes designed to the non-repetitive portion of the genome. See Table 1 for additional design information. From: Optimized design and assessment of whole genome tiling arrays Bioinformatics. 2007;23(13):i195-i204. doi:10.1093/bioinformatics/btm200 Bioinformatics | © 2007 The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

From: Optimized design and assessment of whole genome tiling arrays Fig. 3. Probe selection algorithm. From: Optimized design and assessment of whole genome tiling arrays Bioinformatics. 2007;23(13):i195-i204. doi:10.1093/bioinformatics/btm200 Bioinformatics | © 2007 The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

From: Optimized design and assessment of whole genome tiling arrays Fig. 2. The distribution of U with respect to the number of genome-wide hybridization-quality BLAT alignments for a large set of 50mer probes. The box-and-whiskers plot represents the median value of U by a bold line and the first and third quartiles of the U distribution are represented by the outline of the box. Whiskers represent the largest and smallest values of U within 1.5 × IQR (inter quartile range). From: Optimized design and assessment of whole genome tiling arrays Bioinformatics. 2007;23(13):i195-i204. doi:10.1093/bioinformatics/btm200 Bioinformatics | © 2007 The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.