Comparative Genomics Tools Applied to Bioterrorism Defence
2003, Briefings in Bioinformatics
Abstract
Tom Slezak has BS and MS degrees in computer science and has led the LLNL bioinformatics efforts since 1978.
References (32)
- CDC National Center for Infectious Diseases (URL: http://www.cdc.gov/ncidod/ index.htm).
- Madigan, M. T., Martinko, J. M. and Parker, J. (2000), 'Brock Biology of Microorganisms', 9th Edition, Prentice Hall, Upper Saddle River, NJ.
- Fitch, J. P., Gardner, S. N., Kuczmarski, T. A. et al. (2002), 'Rapid development of nucleic acid diagnostics', Proc. IEEE, Vol. 90(11), pp. 1708-1721.
- URL: http://www.appliedbiosystems.com/ support/tutorials/pcropt/
- CDC Threat List (URL: http:// www.bt.cdc.gov/Agent/agentlist.asp).
- Joint Genome Institute (URL: http://www.jgi.doe.gov).
- Sanger Centre (URL: http://www.sanger.ac.uk)/
- Ho ¨hl, M., Kurtz, S. and Ohlebusch, E. (2002), 'Efficient multiple genome alignment', Bioinformatics, 18(Suppl. 1), pp. S312-S320.
- Morgenstern, B., Dress, A. and Werner, T. (1996), 'Multiple DNA and protein sequence alignment based on segment-to-segment comparison', Proc. Natl Acad. Sci. USA, Vol. 93, pp. 12098-12103.
- Delcher, A. L., Kasif, S., Fleischmann, R. D. et al. (1999), 'Alignment of whole genomes', Nucleic Acids Res., Vol. 27(11), pp. 2369-2376.
- Delcher, A., Phillippy, A., Carlton, J. and Salzberg, S. L. (2002), 'Fast algorithms for large-scale genome alignment and comparison', Nucleic Acids Res., Vol. 30, pp. 2478-2483.
- Kurtz, S. (2003), 'A Time and Space Efficient Algorithm for the Substring Matching Problem', Technical Report, Zentrum fu ¨r Bioinformatik, Universita ¨t Hamburg.
- Altschul, S., Madden, T., Schaffer, A. et al. (1997), 'Gapped BLAST and PSI-BLAST: A new generation of protein database search programs', Nucleic Acids Res., Vol. 25, pp. 3389-3402.
- Primer3 (URL: http:// www-genome.wi.mit.edu/genome_software/ other/primer3.html).
- Cepheid (URL: http://www.cepheid.com/ pages/td_system.html).
- Badger, J. and Olsen, G. (1999), 'CRITICA: Coding region identification tool invoking comparative analysis', Mol. Biol. Evol., Vol. 4, pp. 512-524.
- Borodovsky, M., McIninch, J., Koonin, E. et al. (1995), 'Detection of new genes in a bacterial genome using Markov models for three gene classes', Nucleic Acids Res., Vol. 17, pp. 3554-3562.
- Molecular Beacon (URL: http:// www.idtdna.com/program/techbulletins/ Molecular_Beacons.asp).
- Zemla, A., Slezak, T., Barsky, D. et al. (2003), 'Automated 3D protein structure predictions based on sensitive identification of sequence homology' (unpublished computer program under development at LLNL).
- Protein Data Bank (URL: http:// www.rcsb.org/pdb/).
- Smith, T. F. and Waterman, M. S. (1981), 'Identification of common molecular subsequences', J. Mol. Biol., Vol. 147(1), pp. 195-197.
- Pearson, W. R. (1991). 'Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith- Waterman and FASTA algorithms', Genomics, Vol. 11, pp. 635-650.
- Altschul, S. F., Madden, T. L., Schaffer, A. A. et al. (1997). 'Gapped BLAST and PSI- BLAST: A new generation of protein database search programs', Nucleic Acids Res., Vol. 25(17), pp. 3389-3402.
- Zemla, A. (2002), 'LGA program: A method for finding 3-D similarities in protein structures' (paper in preparation, server accessed at http://PredictionCenter.llnl.gov/ local/lga).
- Bower, M., Cohen, F. E. and Dunbrack, R. L. Jr (1997), 'Sidechain prediction from a backbone-dependent rotamer library: A new tool for homology modeling', J. Mol. Biol., Vol. 267, pp. 1268-1282.
- Rost, B. and Sander, C. (1994), 'Conservation and prediction of solvent accessibility in protein families', Proteins, Vol. 20, pp. 216- 226 (URL: http://cubic.bioc.columbia.edu/ predictprotein/predictprotein.html).
- Hubbard, S. J. and Thornton, J. M. (1993), 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London (URL: http://wolf.bms.umist.ac.uk/naccess/).
- CDC Laboratory Response Network (URL: http://www.phppo.cdc.gov/nltn/pdf/ LRN99.pdf ).
- USDA Plum Island (URL: http:// www.ars.usda.gov/plum/).
- Gardner, S., Kuczmarski, T. A., Vitalis, E. A. and Slezak, T. ( 2003), 'Limitations of TaqMan 1 PCR for detecting divergent viral pathogens illustrated by Hepatitis A, B, C, E and HIV viruses and Human Immunodeficiency Virus', in press.
- West Nile Virus transmission via blood transfusion (URL: http://www.cdc.gov/od/ oc/media/pressrel/r020927d.htm).
- Listeria outbreak (URL: http:// www.fsis.usda.gov/OA/recalls/prelease/ pr090-2002.htm).