Abstract
Discovery of molecular markers for efficient identification of living organisms remains a challenge of high interest. The diversity of species can now be observed in details with low cost genomic sequences produced by new generation of sequencers. A method, called c-GAMMA, is proposed. It formalizes the design of new markers for such data. It is based on a series of filters on forbidden pairs of words, followed by an optimization step on the discriminative power of candidate markers.
First results are presented on a set of microbial genomes. The importance of further developments are stressed to face the huge amounts of data that will soon become available in all kingdoms of life.
Chapter PDF
References
Fleischmann, R., Adams, M., White, O., Clayton, R., Kirkness, E., Kerlavage, A., Bult, C., Tomb, J., Dougherty, B., Merrick, J., et al.: Whole-genome random sequencing and assembly of haemophilus influenzae rd. Science 269(5223), 496–512 (1995)
Koonin, E., Wolf, Y.: Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucl. Acids Res. 36(21), 6688–6719 (2008)
Koonin, E.: Darwinian evolution in the light of genomics. Nucl. Acids Res. 37(4), 1011–1034 (2009)
Cole, J., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R., Kulam-Syed-Mohideen, A., McGarrell, D., Marsh, T., Garrity, G., Tiedje, J.: The ribosomal database project: improved alignments and new tools for rrna analysis. Nucl. Acids Res. 37(suppl. 1), D141–D145 (2009)
Stackebrandt, E., Frederiksen, W., Garrity, G., Grimont, P., Kampfer, P., Maiden, M., Nesme, X., Rossello-Mora, R., Swings, J., Truper, H., Vauterin, L., Ward, A., Whitman, W.: Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52(3), 1043–1047 (2002)
Ratnasingham, S., Hebert, P.: Bold: the barcode of life data system. Mol. Ecol. Notes (2007)
Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S., Jobb, G., Forster, W., Brettske, I., Gerber, S., Ginhart, A.W., Gross, O., Grumann, S., Hermann, S., Jost, R., Konig, A., Liss, T., Lubmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., Schleifer, K.H.: Arb: a software environment for sequence data. Nuc. Acids Res. 32(4), 1363–1371 (2004)
Pozhitkov, A., Tautz, D.: An algorithm and program for finding sequence specific oligonucleotide probes for species identification. BMC Bioinformatics 3(9) (2002)
Kampke, T., Kieninger, M., Mecklenburg, M.: Efficient primer design algorithms. Bioinformatics 17(3), 214–225 (2001)
Kaderali, L., Schliep, A.: Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics 18(10), 1340–1349 (2002)
Lemoine, S., Combes, F., Le Crom, S.: An evaluation of custom microarray applications: the oligonucleotide design challenge. Nuc. Acids Res. 37(6), 1726–1739 (2009)
Wang, J., Li, K., Sung, W.: G-primer: greedy algorithm for selecting minimal primer set. Bioinformatics 20(15), 2473–2475 (2004)
Liu, Y., Carson, D.: A novel approach for determining cancer genomic breakpoints in the presence of normal DNA. PLoS One 2(4) (2007)
Bashir, A., Liu, Y.T., Raphael, B.J., Carson, D., Bafna, V.: Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics 23(21), 2807–2815 (2007)
SantaLucia, J.J.: A unified view of polymer, dumbbell, and oligonucleotide dna nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95(4), 1460–1465 (1998)
Bailey, T.L., Elkan, C.: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28–36 (1994)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Peterlongo, P., Nicolas, J., Lavenier, D., Vorc’h, R., Querellou, J. (2009). c-GAMMA:Comparative Genome Analysis of Molecular Markers. In: Kadirkamanathan, V., Sanguinetti, G., Girolami, M., Niranjan, M., Noirel, J. (eds) Pattern Recognition in Bioinformatics. PRIB 2009. Lecture Notes in Computer Science(), vol 5780. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04031-3_23
Download citation
DOI: https://doi.org/10.1007/978-3-642-04031-3_23
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-04030-6
Online ISBN: 978-3-642-04031-3
eBook Packages: Computer ScienceComputer Science (R0)