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Thus, a flexible and efficient tiling array design approach is still needed and could assist in various types and scales of transcriptomic experiment.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this paper, we address issues and challenges in designing probes suitable for tiling array applications and targeted sequencing. In particular, we define the penalized uniqueness score, which serves as a controlling criterion to eliminate potential cross-hybridization, and a flexible tiling array design pipeline. Unlike BLAST or simple suffix array based methods, computing and using our uniqueness measurement can be more efficient for large scale design and require less memory. The parameters provided could assist in various types of genomic tiling task. In addition, using both commercial array data and experiment data we show, unlike previously claimed, that palindromic sequence exhibiting relatively lower uniqueness.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our proposed penalized uniqueness score could serve as a better indicator for cross hybridization with higher sensitivity and specificity, giving more control of expected array quality. The flexible tiling design algorithm incorporating the penalized uniqueness score was shown to give higher coverage and resolution. The package to calculate the penalized uniqueness score and the described probe selection algorithm are implemented as a Perl program, which is freely available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www1.fbn-dummerstorf.de\/en\/forschung\/fbs\/fb3\/paper\/2012-yang-1\/OTAD.v1.1.tar.gz\" ext-link-type=\"uri\">http:\/\/www1.fbn-dummerstorf.de\/en\/forschung\/fbs\/fb3\/paper\/2012-yang-1\/OTAD.v1.1.tar.gz<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-323","type":"journal-article","created":{"date-parts":[[2012,12,5]],"date-time":"2012-12-05T18:12:05Z","timestamp":1354731125000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Flexible and efficient genome tiling design with penalized uniqueness score"],"prefix":"10.1186","volume":"13","author":[{"given":"Yang","family":"Du","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eduard","family":"Murani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siriluck","family":"Ponsuksili","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Klaus","family":"Wimmers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,12,5]]},"reference":[{"issue":"5569","key":"5673_CR1","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1126\/science.1068597","volume":"296","author":"P Kapranov","year":"2002","unstructured":"Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SPA, Gingeras TR: Large-Scale Transcriptional Activity in Chromosomes 21 and 22. 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