Title :
Nonoverlapping Clone Pooling for High-Throughput Sequencing
Author :
Kuroshu, Reginaldo M.
Author_Institution :
Inst. de Cienc. e Tecnol., Univ. Fed. de Sao Paulo, Sao Josedos Campos, Brazil
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.
Keywords :
DNA; bioinformatics; genetics; genomics; molecular biophysics; bin-packing algorithms; clone-based sequencing methods; constant absolute worst-case ratios; fosmid clone sequencing; full-length cDNA sequencing; genome; graph coloring algorithms; high-throughput sequencing; nonoverlapping clone pooling problem; second-generation sequencers; spliced transcripts; structural variation identification; Approximation algorithms; Approximation methods; Bioinformatics; Cloning; Genomics; Sequential analysis; Bin-packing; graph coloring; next-generation sequencing; nonoverlapping clone pooling;
Journal_Title :
Computational Biology and Bioinformatics, IEEE/ACM Transactions on
DOI :
10.1109/TCBB.2013.83