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.
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
Almeida, N.F.: Tools for genome comparison (In Portuguese) PhD thesis, IC-Unicamp, Campinas-SP, Brazil (2002)
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)
AraĂºjo, F.R., Almeida, N.F., Adi, S.S., et al.: Functional characterization of Anaplasma marginale and identification of antigens (in preparation)
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)
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)
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)
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)
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)
Setubal, J.C., Wernec, R.: A program for building contig scaffolds in double-barrelled shotgun genome sequencing. Technical report, IC, Unicamp (2001)
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)
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)
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)
Zhang, Z., Schwartz, S., Wagner, L., Miller, W.: A greedy algorithm for aligning dna sequences. J. Comput. Biol. 7(1-2), 203–214 (2000)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
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
Download citation
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)