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Dispensation order generation for pyrosequencing
RISE, Swedish ICT, SICS, Computer Systems Laboratory.ORCID iD: 0000-0003-3079-8095
2004 (English)In: Proceedings. Bioinformatics 2004. Second Asia-Pacific Bioinformatics Conference (APBC2004), 2004, 1, Vol. 29, 5 p.327-332 p.Conference paper, (Refereed)
Abstract [en]

This article describes a dispensation order generation algorithm for genotyping using the Pyrosequencing method. The input template of the algorithm is a slightly restricted regular expression over the DNA strings that can be expected in a given sample. The algorithm computes a dispensation order that allows for determining, for each polymorphism in the input template, the genotype of any sample. The algorithm has the structure of a non-deterministic rewrite system, which gives rise to a search tree. We show that within any branch of the search tree, the rewrite system is confluent and terminating. We use nogood generation and limited discrepancy search to prune the search tree and to focus the search for shorter dispensation orders before looking for longer ones. The algorithm as described herein assumes samples from a diploid genome, but can readily be generalized to general k-ploid genomes.

Place, publisher, year, edition, pages
2004, 1. Vol. 29, 5 p.327-332 p.
National Category
Computer and Information Science
Identifiers
URN: urn:nbn:se:ri:diva-22332ISBN: 1-920682-11-2 (print)OAI: oai:DiVA.org:ri-22332DiVA: diva2:1041877
Conference
Second Asia Pacific Bioinformatics Conference (APBC2004), 18-22 Jan 2004, Dunedin, New Zealand
Note

Published in Bioinformatics 2004, Volume 29; Australian Computer Science Communications, Volume 26, Number 4. Edited by Yi-Ping Phoebe Chen. ISBN-13 1-920682-11-2. ISSN 1445-1336.

Available from: 2016-10-31 Created: 2016-10-31 Last updated: 2017-08-10Bibliographically approved

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