Open Access Methodology article

Flexible and efficient genome tiling design with penalized uniqueness score

Yang Du1, Eduard Murani1, Siriluck Ponsuksili2 and Klaus Wimmers1*

Author Affiliations

1 Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany

2 Research Group Functional Genomics, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany

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BMC Bioinformatics 2012, 13:323  doi:10.1186/1471-2105-13-323

Published: 5 December 2012

Abstract

Background

As a powerful tool in whole genome analysis, tiling array has been widely used in the answering of many genomic questions. Now it could also serve as a capture device for the library preparation in the popular high throughput sequencing experiments. Thus, a flexible and efficient tiling array design approach is still needed and could assist in various types and scales of transcriptomic experiment.

Results

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.

Conclusions

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 http://www1.fbn-dummerstorf.de/en/forschung/fbs/fb3/paper/2012-yang-1/OTAD.v1.1.tar.gz webcite.

Keywords:
Tiling array; Targeted sequencing; Probe design; Penalized uniqueness score