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Nonoverlapping Clone Pooling for High-Throughput Sequencing
Sept.-Oct. 2013 (vol. 10 no. 5)
pp. 1091-1097
Reginaldo M. Kuroshu, Universidade Federal de São Paulo, São José dos Campos
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
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.2013.83
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