Abstract
We propose a way to index population genotype information together with the complete genome sequence, so that one can use the index to efficiently align a given sequence to the genome with all plausible genotype recombinations taken into account. This is achieved through converting a multiple alignment of individual genomes into a finite automaton recognizing all strings that can be read from the alignment by switching the sequence at any time. The finite automaton is indexed with an extension of Burrows-Wheeler transform to allow pattern search inside the plausible recombinant sequences. The size of the index stays limited, because of the high similarity of individual genomes. The index finds applications in variation calling and in primer design.
Access provided by Autonomous University of Puebla. Download to read the full chapter text
Chapter PDF
Similar content being viewed by others
Keywords
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
References
Albers, C.A., et al.: Dindel: Accurate indel calls from short-read data. Genome Research (October 2010)
Burrows, M., Wheeler, D.: A block sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation (1994)
Darling, A.E., et al.: ProgressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. PLoS ONE 5(6), e11147 (2010)
Dean, J., Ghemawat, S.: MapReduce: Simplified data processing on large clusters. In: Proc. OSDI 2004, pp. 137–150. USENIX Association (2004)
Ferragina, P., et al.: Compressing and indexing labeled trees, with applications. Journal of the ACM 57(1), article 4 (2009)
Ferragina, P., Manzini, G.: Indexing compressed text. Journal of the ACM 52(4), 552–581 (2005)
Flicek, P., Birney, E.: Sense from sequence reads: methods for alignment and assembly. Nature Methods 6, S6–S12 (2009)
Grossi, R., Vitter, J.S.: Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM Journal on Computing 35(2), 378–407 (2005)
Lander, E.S., et al.: Initial sequencing and analysis of the human genome. Nature 409(6822), 860–921 (2001)
Langmead, B., et al.: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3), R25 (2009)
Levy, S., et al.: The diploid genome sequence of an individual human. PLoS Biol. 5(10), e254 (2007)
Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 27(14), 1754–1760 (2009)
Li, R., et al.: SOAP2. Bioinformatics 25(15), 1966–1967 (2009)
Li, R., et al.: De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20(2), 265–272 (2010)
Mäkinen, V., et al.: Storage and retrieval of highly repetitive sequence collections. Journal of Computational Biology 17(3), 281–308 (2010)
Mäkinen, V., et al.: Unified view of backward backtracking in short read mapping. In: Elomaa, T., Mannila, H., Orponen, P. (eds.) Ukkonen Festschrift 2010. LNCS, vol. 6060, pp. 182–195. Springer, Heidelberg (2010)
Metzker, M.L.: Sequencing technologies – the next generation. Nature Reviews Genetics 11, 31–46 (2010)
Myers, S., et al.: A fine-scale map of recombination rates and hotspots across the human genome. Science 310(5746), 321–324 (2005)
Navarro, G., Mäkinen, V.: Compressed full-text indexes. ACM Computing Surveys 39(1), 2 (2007)
Puglisi, S.J., et al.: A taxonomy of suffix array construction algorithms. ACM Computing Surveys 39(2), 4 (2007)
Spang, R., et al.: A novel approach to remote homology detection: Jumping alignments. Journal of Computational Biology 9(5), 747–760 (2002)
Venter, J.C., et al.: The sequence of the human genome. Science 291(5507), 1304–1351 (2001)
Wheeler, D.A., et al.: The complete genome of an individual by massively parallel DNA sequencing. Nature 452(7189), 872–876 (2008)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Sirén, J., Välimäki, N., Mäkinen, V. (2011). Indexing Finite Language Representation of Population Genotypes. In: Przytycka, T.M., Sagot, MF. (eds) Algorithms in Bioinformatics. WABI 2011. Lecture Notes in Computer Science(), vol 6833. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23038-7_23
Download citation
DOI: https://doi.org/10.1007/978-3-642-23038-7_23
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-23037-0
Online ISBN: 978-3-642-23038-7
eBook Packages: Computer ScienceComputer Science (R0)