Nonoverlapping Clone Pooling for High-Throughput Sequencing
| dc.contributor.author | Kuroshu, Reginaldo M. | |
| dc.contributor.institution | Universidade Federal de São Paulo (UNIFESP) | |
| dc.date.accessioned | 2016-01-24T14:34:23Z | |
| dc.date.available | 2016-01-24T14:34:23Z | |
| dc.date.issued | 2013-09-01 | |
| dc.description.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. | en |
| dc.description.affiliation | Universidade Federal de São Paulo, Inst Ciencia & Tecnol, BR-12231280 Sao Jose Dos Campos, SP, Brazil | |
| dc.description.affiliationUnifesp | Universidade Federal de São Paulo, Inst Ciencia & Tecnol, BR-12231280 Sao Jose Dos Campos, SP, Brazil | |
| dc.description.source | Web of Science | |
| dc.description.sponsorship | Japanese Government Ministry of Education, Culture, Sports, Science, and Technology (MEXT) | |
| dc.description.sponsorship | Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) | |
| dc.format.extent | 1091-1097 | |
| dc.identifier | http://dx.doi.org/10.1109/TCBB.2013.83 | |
| dc.identifier.citation | Ieee-acm Transactions On Computational Biology and Bioinformatics. Los Alamitos: Ieee Computer Soc, v. 10, n. 5, p. 1091-1097, 2013. | |
| dc.identifier.doi | 10.1109/TCBB.2013.83 | |
| dc.identifier.issn | 1545-5963 | |
| dc.identifier.uri | http://repositorio.unifesp.br/handle/11600/36728 | |
| dc.identifier.wos | WOS:000331461400002 | |
| dc.language.iso | eng | |
| dc.publisher | Ieee Computer Soc | |
| dc.relation.ispartof | Ieee-acm Transactions On Computational Biology and Bioinformatics | |
| dc.rights | info:eu-repo/semantics/restrictedAccess | |
| dc.rights.license | http://www.ieee.org/publications_standards/publications/rights/rights_policies.html | |
| dc.subject | Bin-packing | en |
| dc.subject | graph coloring | en |
| dc.subject | next-generation sequencing | en |
| dc.subject | nonoverlapping clone pooling | en |
| dc.title | Nonoverlapping Clone Pooling for High-Throughput Sequencing | en |
| dc.type | info:eu-repo/semantics/article |