Summary
The same high-throughput techniques used to make genomic sequences generally available, are also useful in mapping the genetic differences between individuals. Resequencing of a genomic region in a set of individuals is considered the golden standard for the discovery of sequence variants. However, with the available high-throughput sequencing technology data analysis has become the rate-limiting step in data management and analysis of large resequencing projects. To solve this issue we developed a software package novoSNP that conscientiously discovers single nucleotide polymorphisms and insertion-deletion polymorphisms in sequence trace files in a fast, reliable and user friendly way. Furthermore, it can also be used to create databases containing annotated reference sequences, add and align trace data, keep track of validation status of variants, annotate variants, and produce reports on validated variants and genotypes. novoSNP is available from http://www.molgen.ua.ac.be/bioinfo/novosnp. There are versions for MS Windows as well as Linux
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References
Adams, M. D., Celniker, S. E., Holt, R. A., et al. (2000) The genome sequence of Drosophila melanogaster. Science 287, 2185–2195.
Lander, E. S., Linton, L. M., Birren, B., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.
The C. elegans Sequencing Consortium. (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018.
Venter, J. C., Adams, M. D., Myers, E. W., et al. (2001) The sequence of the human genome. Science 291, 1304–1351.
Waterston, R. H., Lindblad-Toh, K., Birney, E., et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562.
Kwok, P. Y., Carlson, C., Yager, T. D., Ankener, W., and Nickerson, D. A. (1994) Comparative analysis of human DNA variations by fluorescence-based sequencing of PCR products. Genomics 23, 138–144.
Weckx, S., Del-Favero, J., Rademakers, R., Claes, L., et al. (2005) novoSNP, a novel computational tool for sequence variation discovery. Genome Res. 15, 436–442.
Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194.
Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185.
Wheelan, S. J., Church, D. M., and Ostell, J. M. (2001) Spidey: a tool for mRNA-to-genomic alignments. Genome Res. 11, 1952–1957
Acknowledgments
This work was in part funded by the Special Research Fund of the University of Antwerp, the Fund for Scientific Research Flanders (FWO-V), the Interuniversity Attraction Poles program P5/19 of the Belgian Federal Science Policy Office.
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Rijk, P.D., Del-Favero, J. (2007). novoSNP3. In: Bergman, N.H. (eds) Comparative Genomics. Methods In Molecular Biology™, vol 396. Humana Press. https://doi.org/10.1007/978-1-59745-515-2_21
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DOI: https://doi.org/10.1007/978-1-59745-515-2_21
Publisher Name: Humana Press
Print ISBN: 978-1-934115-37-4
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