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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 4, Issue 3

Issues

Mining for Single Nucleotide Polymorphisms in Expressed Sequence Tags of European Sea Bass

E. L. Souche
  • Corresponding author
  • Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
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/ B. Hellemans
  • Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ J. K. J. Van Houdt
  • Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
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  • De Gruyter OnlineGoogle Scholar
/ A. Canario
  • Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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/ S. Klages / R. Reinhardt / F. A. M. Volckaert
  • Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
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  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2007-73

Abstract

As a multitude of sequence data are published, discovering polymorphisms bioinformatically becomes a valid option. In silico Single Nucleotide Polymorphism (SNP) detection is based on the analysis of multiple alignments. Each column of an alignment is considered a slice containing one base of every sequence aligned. If a mismatch is detected, the slice is further analysed and the mismatch may be reported as a candidate SNP.

About 30,000 Expressed Sequence Tags (ESTs) of the fish European sea bass have been sequenced and processed. Since ESTs are redundant, they provide a resource for in silico SNP discovery. To prevent the detection of sequencing errors, a redundancy of two is chosen in order for a mismatch to be considered a candidate SNP. Among the various tools available to detect candidate SNPs, three software packages were tested: SNPServer, PolyBayes and PolyFreq. Candidate SNPs were validated in the laboratory by cloning and sequencing. From preliminary results PolyFreq outperforms both PolyBayes and SNPServer in terms of positive predictive value and SNPServer is the most sensitive tool. PolyFreq and SNPServer non-default identify respectively the fewest and highest number of candidates. Considering candidates detected by several tools seems to enhance both positive predictive value and sensitivity. Out of the 69 loci sequenced, only four were monomorphic, leading to a total of 91.3% polymorphic loci. Randomly chosen contigs will be sequenced to know whether SNP discovery tools tend to predict polymorphic fragments. Polymorphisms will be mapped, used for selection in aquaculture and the study of adaptation in natural populations.

About the article

Published Online: 2016-10-18

Published in Print: 2007-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 4, Issue 3, Pages 158–167, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2007-73.

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© 2007 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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