Abstract
DNA sequencing is an important tool for discovery of genetic variants. The task of detecting single-nucleotide variants is complicated by noise and sequencing artifacts in sequencing data. Several in silico tools have been developed to assist this process. These tools interpret the raw chromatogram data and perform a specialized base-calling and quality-control assessment procedure to identify variants. The approach used to identify variants differs between the tools, with some specific to SNPs and other for Indels. The choice of a tool is guided by the design of the sequencing project and the nature of the variant to be discovered. In this chapter, these tools are compared to facilitate the choice of a tool used for variant discovery.
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References
Sanger, F., Nicklen, S., Coulson, A. R. (1992) DNA sequencing with chain-terminating inhibitors. 1977, Biotechnology 24, 104–108.
MacBeath, J. R., Harvey, S. S., Oldroyd, N. J. (2001) Automated fluorescent DNA sequencing on the ABI PRISM 377, Methods Mol Biol 167, 119–152.
Marth, G. T., Korf, I., Yandell, M. D., Yeh, R. T., Gu, Z., Zakeri, H., Stitziel, N. O., Hillier, L., Kwok, P. Y., Gish, W. R. (1999) A general approach to single-nucleotide polymorphism discovery, Nat Genet 23, 452–456.
Takahashi, M., Matsuda, F., Margetic, N., Lathrop, M. (2003) Automated identification of single nucleotide polymorphisms from sequencing data, J Bioinform Comput Biol 1, 253–265.
Zhang, J., Wheeler, D. A., Yakub, I., Wei, S., Sood, R., Rowe, W., Liu, P. P., Gibbs, R. A., Buetow, K. H. (2005) SNPdetector: a software tool for sensitive and accurate SNP detection, PLoS Comput Biol 1, e53.
Weckx, S., Del-Favero, J., Rademakers, R., Claes, L., Cruts, M., De Jonghe, P., Van Broeckhoven, C., De Rijk, P. (2005) novoSNP, a novel computational tool for sequence variation discovery, Genome Res 15, 436–442.
Manaster, C., Zheng, W., Teuber, M., Wachter, S., Doring, F., Schreiber, S., Hampe, J. (2005) InSNP: a tool for automated detection and visualization of SNPs and InDels, Hum Mutat 26, 11–19.
Crowe, M. L. (2005) SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms, BMC Bioinformatics 6, 133.
Ewing, B., Green, P. (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities, Genome Res 8, 186–194.
Dicks, E., Teague, J. W., Stephens, P., Raine, K., Yates, A., Mattocks, C., Tarpey, P., Butler, A., Menzies, A., Richardson, D., Jenkinson, A., Davies, H., Edkins, S., Forbes, S., Gray, K., Greenman, C., Shepherd, R., Stratton, M. R., Futreal, P. A., Wooster, R. (2007) AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes, Bioinformatics 23, 1689–1691.
Chen, K., McLellan, M. D., Ding, L., Wendl, M. C., Kasai, Y., Wilson, R. K., Mardis, E. R. (2007) PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data, Genome Res 17, 659–666.
Ngamphiw, C., Kulawonganunchai, S., Assawamakin, A., Jenwitheesuk, E., Tongsima, S. (2008) VarDetect: a nucleotide sequence variation exploratory tool, BMC Bioinformatics 9 Suppl 12, S9.
Wegrzyn, J. L., Lee, J. M., Liechty, J., Neale, D. B. (2009) PineSAP – sequence alignment and SNP identification pipeline, Bioinformatics 25, 2609–2610.
Bhangale, T. R., Stephens, M., Nickerson, D. A. (2006) Automating resequencing-based detection of insertion-deletion polymorphisms, Nat Genet 38, 1457–1462.
Nickerson, D. A., Tobe, V. O., Taylor, S. L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing, Nucleic Acids Res 25, 2745–2751.
Staden, R. (1996) The Staden sequence analysis package, Mol Biotechnol 5, 233–241.
Seroussi, E., Ron, M., Kedra, D. (2002) ShiftDetector: detection of shift mutations, Bioinformatics 18, 1137–1138.
Dmitriev, D. A., Rakitov, R. A. (2008) Decoding of superimposed traces produced by direct sequencing of heterozygous indels, PLoS Comput Biol 4, e1000113.
Smith, T. F., Waterman, M. S. (1981) Identification of common molecular subsequences, J Mol Biol 147, 195–197.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. (1990) Basic local alignment search tool, J Mol Biol 215, 403–410.
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Tongsima, S., Assawamakin, A., Piriyapongsa, J., Shaw, P.J. (2011). Comparative View of In Silico DNA Sequencing Analysis Tools. In: Yu, B., Hinchcliffe, M. (eds) In Silico Tools for Gene Discovery. Methods in Molecular Biology, vol 760. Humana Press. https://doi.org/10.1007/978-1-61779-176-5_13
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DOI: https://doi.org/10.1007/978-1-61779-176-5_13
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