CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013 vol.10 Issue No.05 - Sept.-Oct.

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Issue No.05 - Sept.-Oct. (2013 vol.10)

pp: 1091-1097

Reginaldo M. Kuroshu , Inst. de Cienc. e Tecnol., Univ. Fed. de Sao Paulo, Sao Josedos Campos, Brazil

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.83

ABSTRACT

Simultaneously sequencing multiple clones using second-generation sequencers can speed up many essential clone-based sequencing methods. However, in applications such as fosmid clone sequencing and full-length cDNA sequencing, it is important to create pools of clones that do not overlap on the genome for the identification of structural variations and alternatively spliced transcripts, respectively. We define the nonoverlapping clone pooling problem and provide practical solutions based on optimal graph coloring and bin-packing algorithms with constant absolute worst-case ratios, and further extend them to cope with repetitive mappings. Using theoretical analysis and experiments, we also show that the proposed methods are applicable.

INDEX TERMS

Cloning, Bioinformatics, Sequential analysis, Genomics, Approximation methods, Approximation algorithms,nonoverlapping clone pooling, Bin-packing, graph coloring, next-generation sequencing

CITATION

Reginaldo M. Kuroshu, "Nonoverlapping Clone Pooling for High-Throughput Sequencing",

*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, vol.10, no. 5, pp. 1091-1097, Sept.-Oct. 2013, doi:10.1109/TCBB.2013.83REFERENCES