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Mapping Contigs onto Reference Genomes

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Advances in Bioinformatics and Computational Biology (BSB 2007)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4643))

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Abstract

This work presents a preliminary comparative study of some tools for mapping annotated contigs onto a close-related complete annotated genome. This kind of mapping could help scientists in generating additional sequences to fill in gaps in finishing genome projects, or even in getting relevant functional information, specially when annotations of the complete genome and contigs are available.

This work was supported by CNPq and Fundect-MS.

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References

  1. Almeida, N.F.: Tools for genome comparison (In Portuguese) PhD thesis, IC-Unicamp, Campinas-SP, Brazil (2002)

    Google Scholar 

  2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acid Research 25, 3389–3402 (1997)

    Article  Google Scholar 

  3. AraĂºjo, F.R., Almeida, N.F., Adi, S.S., et al.: Functional characterization of Anaplasma marginale and identification of antigens (in preparation)

    Google Scholar 

  4. Brayton, K.A., Kappmeyer, L.S., Herndon, D.R., Dark, M.J., Tibbals, D.L., Palmer, G.H., McGuire, T.C., Knowles Jr., D.P.: Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins. Proc. Natl. Acad. Sci. USA 102(3), 844–849 (2005)

    Article  Google Scholar 

  5. da Silva, A.C.R., Setubal, J.C., Almeida, N.F., et al.: Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417(6887), 459–463 (2002)

    Article  Google Scholar 

  6. Delcher, A.L., Kasif, S., Fleischmann, R.D., Peterson, J., White, O., Salzberg, S.L.: Alignment of whole genomes. Nucleic Acids Research 27(11), 2369–2376 (1999)

    Article  Google Scholar 

  7. Delcher, A.L., Phillippy, A., Carlton, J., Salzberg, S.L.: Fast algorithms for large-scale genome alignment and comparison. NAR 30(11), 2478–2483 (2002)

    Article  Google Scholar 

  8. Monteiro-Vitorello, C.B., Camargo, L.E.A., Setubal, J.C., Almeida, N.F., et al.: The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli. Molelular Plant-Microbe Interactions 17(8), 827–836 (2004)

    Article  Google Scholar 

  9. Setubal, J.C., Wernec, R.: A program for building contig scaffolds in double-barrelled shotgun genome sequencing. Technical report, IC, Unicamp (2001)

    Google Scholar 

  10. Van Sluys, M.A., Setubal, J.C., Almeida, N.F., et al.: Comparative analyses of the complete genome sequences of pierce’s disease and citrus variegated chlorosis strains of Xylella fastidiosa. J. Bacteriology 185(3), 1018–1026 (2003)

    Article  Google Scholar 

  11. Stein, L.D., Mungall, C., et al.: The generic genome browser: a building block for a model organism system database. Genome Res. 12(10), 1599–1610 (2002)

    Article  Google Scholar 

  12. Wood, D.W., Setubal, J.C., Almeida, N.F., et al.: The genome of the natural genetic engineer Agrobacterium tumefaciens c58. Science 294, 2317–2323 (2001)

    Article  Google Scholar 

  13. Zhang, Z., Schwartz, S., Wagner, L., Miller, W.: A greedy algorithm for aligning dna sequences. J. Comput. Biol. 7(1-2), 203–214 (2000)

    Article  Google Scholar 

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Marie-France Sagot Maria Emilia M. T. Walter

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© 2007 Springer-Verlag Berlin Heidelberg

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Almeida, N.F. et al. (2007). Mapping Contigs onto Reference Genomes. In: Sagot, MF., Walter, M.E.M.T. (eds) Advances in Bioinformatics and Computational Biology. BSB 2007. Lecture Notes in Computer Science(), vol 4643. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73731-5_15

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  • DOI: https://doi.org/10.1007/978-3-540-73731-5_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-73730-8

  • Online ISBN: 978-3-540-73731-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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