Abstract
Here we present RAIDER, a tool for the de novo identification of elementary repeats. The problem of searching for genomic repeats without reference to a compiled profile library is important in the annotation of new genomes and the discovery of new repeat classes. Several tools have attempted to address the problem, but generally suffer either an inability to run at the whole-genome scale or loss of sensitivity due to sequence variation between repeat copies. To address this, Zheng and Lonardi define elementary repeats: building blocks that can be assembled into a repeat library, but allow for the filtering of spurious fragments. However, their tool was too slow for use on large input, and subsequent attempts to improve efficiency have been unable to deal with the expected variation between repeat instances. RAIDER addresses both these problems, implementing a novel algorithm for elementary repeat detection and incorporating the spaced seed strategy of PatternHunter to allow for copy variation. Able to process the human genome in under 6.4 hours, initial results indicate a coverage rate comparable to or better than that achieved by competing de novo search tool when paired with the library-based RepeatMasker.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Smit, A.F.A., Hubley, R., Green, P.: RepeatMasker Open-1.0 (1996-2010), http://www.repeatmasker.org
Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25(17), 3389 (1997)
Bao, Z., Eddy, S.R.: Automated de novo identification of repeat sequence families in sequenced genomes. Genome Research 12(8), 1269–1276 (2002)
Bergman, C.M., Quesneville, H.: Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics 8(6), 382–392 (2007)
Edgar, R.C., Myers, E.W.: PILER: identification and classification of genomic repeats. Bioinformatics 21(suppl. 1), i152–i158 (2005)
Google: sparsehash - An extremely memory-efficient hash_map implementation - Google Project Hosting, http://code.google.com/p/sparsehash/
Hardison, R.C.: Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution. Genome Research 13(1), 13–26 (2003)
He, D.: Using suffix tree to discover complex repetitive patterns in DNA sequences. In: Conference Proceedings: ... of Annual International Conference of the IEEE Engineering in Medicine and Biology Society, vol. 1, pp. 3474–3477. IEEE Engineering in Medicine and Biology Society (2006)
Huo, H., Wang, X., Stojkovic, V.: An Adaptive Suffix Tree Based Algorithm for Repeats Recognition in a DNA Sequence. Bioinformatics and Bioengenierring, 181–184 (2009)
Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., Walichiewicz, J.: Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research 110(1-4), 462–467 (2005)
Karro, J.E., Peifer, M., Hardison, R.C., Kollmann, M., von Grünberg, H.H.: Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure. Molecular Biology and Evolution 25(2), 362–374 (2008)
Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J., Giegerich, R.: REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 29(22), 4633–4642 (2001)
Lander, E.S., et al.: Initial sequencing and analysis of the human genome. Nature 409(6822), 860–921 (2001)
Li, M., Ma, B., Kisman, D., Tromp, J.: Patternhunter II: highly sensitive and fast homology search. Journal of Bioinformatics and Computational Biology 2(3), 417–439 (2004)
Li, R., Ye, J., Li, S., Wang, J., Han, Y., Ye, C., Wang, J., Yang, H., Yu, J., Wong, G.K.S., Wang, J.: ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Computational Biology 1(4), e43 (2005)
Ma, B., Tromp, J., Li, M.: PatternHunter: faster and more sensitive homology search. Bioinformatics (2002)
Pevzner, P.A., Tang, H., Tesler, G.: De novo repeat classification and fragment assembly. Genome Research 14(9), 1786–1796 (2004)
Price, A.L., Jones, N.C., Pevzner, P.A.: De novo identification of repeat families in large genomes. Bioinformatics 21(suppl. 1), i351–8 (2005)
Saha, S., Bridges, S., Magbanua, Z.V., Peterson, D.G.: Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences. Tropical Plant Biology 1(1), 85–96 (2008)
Saha, S., Bridges, S., Magbanua, Z.V., Peterson, D.G.: Empirical comparison of ab initio repeat finding programs. Nucleic Acids Research 36(7), 2284–2294 (2008)
Zabala, G., Vodkin, L.: Novel exon combinations generated by alternative splicing of gene fragments mobilized by a CACTA transposon in Glycine max. BMC Plant Biology 7, 38 (2007)
Zerbino, D.R., Birney, E.: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18(5), 821–829 (2008)
Zheng, J., Lonardi, S.: Discovery of repetitive patterns in DNA with accurate boundaries … (2005)
Zhi, D., Raphael, B.J., Price, A.L., Tang, H., Pevzner, P.A.: Identifying repeat domains in large genomes. Genome Biology 7(1), R7 (2006)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer International Publishing Switzerland
About this paper
Cite this paper
Figueroa, N., Liu, X., Wang, J., Karro, J. (2013). RAIDER: Rapid Ab Initio Detection of Elementary Repeats. In: Setubal, J.C., Almeida, N.F. (eds) Advances in Bioinformatics and Computational Biology. BSB 2013. Lecture Notes in Computer Science(), vol 8213. Springer, Cham. https://doi.org/10.1007/978-3-319-02624-4_16
Download citation
DOI: https://doi.org/10.1007/978-3-319-02624-4_16
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-02623-7
Online ISBN: 978-3-319-02624-4
eBook Packages: Computer ScienceComputer Science (R0)