Palindromes in SARS and Other Coronaviruses

References

• Bloom B. R. Lessons from SARS. Science (2003) 300:701Crossref, Google Scholar
• Cain D., Erlwein O., Grigg A., Russell R. A., McClure M. O. Palindromic sequence plays a critical role in human foamy virus dimerization. J. Virology (2001) 75:3731–3739Crossref, Google Scholar
• Dirac A. M., Huthoff H., Kjems J., Berkhout B. Requirements for RNA heterodimerization of the human immunodeficiency virus type 1 (HIV-1) and HIV-2 genomes. J. General Virology (2002) 83:2533–2542Crossref, Google Scholar
• Giedroc D. P., Theimer C. A., Nixon P. L. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J. Molecular Biol. (2000) 298:167–185Crossref, Google Scholar
• Hill M. K., Shehu-Xhilaga M., Campbell S. M., Poumbourios P., Crowe S. M., Mak J. The dimer initiation sequence stem-loop of Human Immunodeficiency Virus Type 1 is dispensable for viral replication in peripheral blood mononuclear cells. J. Virology (2003) 77:8329–8335Crossref, Google Scholar
• Karlin S., Burge C., Campbell A. M. Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucleic Acids Res. (1992) 20:1363–1370Crossref, Google Scholar
• Leung M. Y., Choi K. P., Xia A., Chen L. H. Y. Nonrandom clusters of palindromes in herpesvirus genomes. (2002) (National University of Singapore, Singapore) . IMS preprint series 2002-2, Institute for Mathematical SciencesGoogle Scholar
• Marra M. A., Jones S. J., Astell C. R., Holt R. A., Brooks-Wilson A., Butterfield Y. S., Khattra J., Asano J. K., Barber S. A., Chan S. Y., Cloutier A., Coughlin S. M., Freeman D., Girn N., Griffith O. L., Leach S. R., Mayo M., McDonald H., Montgomery S. B., Pandoh P. K., Petrescu A. S., Robertson A. G., Schein J. E., Siddiqui A., Smailus D. E., Stott J. M., Yang G. S., Plummer F., Andonov A., Artsob H., Bastien N., Bernard K., Booth T. F., Bowness D., Czub M., Drebot M., Fernando L., Flick R., Garbutt M., Gray M., Grolla A., Jones S., Feldmann H., Meyers A., Kabani A., Li Y., Normand S., Stroher U., Tipples G. A., Tyler S., Vogrig R., Ward D., Watson B., Brunham R. C., Krajden M., Petric M., Skowronski D. M., Upton C., Roper R. L. The genome sequence of the SARS-associated coronavirus. Science (2003) 300:1399–1404Crossref, Google Scholar
• Merkl R., Fritz H. J. Statistical evidence for a biochemical pathway of natural, sequence-targeted G/C to C/G transversion mutagenesis in. Haemophilus influenzae Rd. Nucleic Acids Res. (1996) 24:4146–4151Crossref, Google Scholar
• Qin L., Xiong B., Luo C., Guo Z. M., Hao P., Su J., Nan P., Feng Y., Shi Y. X., Yu X. J., Luo X. M., Chen K. X., Shen X., Shen J. H., Zou J. P., Zhao G. P., Shi T. L., He W. Z., Zhong Y., Jiang H. L., Li Y. X. Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis. Acta Pharmacologica Sinica (2003) 24:489–496Google Scholar
• Rice P., Longden I., Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genetics (2000) 16:276–277Crossref, Google Scholar
• Robin S., Daudin J. J. Exact distribution of word occurrences in a random sequence of letters. J. Appl. Probab. (1999) 36:179–193Crossref, Google Scholar
• Rocha E. P., Danchin A., Viari A. Evolutionary role of restriction/modification systems as revealed by comparative genome analysis. Genome Res. (2001) 11:946–958Crossref, Google Scholar
• Rocha E. P., Viari A., Danchin A. Oligonucleotide bias in Bacillus subtilis: General trends and taxonomic comparisons. Nucleic Acids Res. (1998) 26:2971–2980Crossref, Google Scholar
• Rota P. A., Oberste M. S., Monroe S. S., Nix W. A., Campagnoli R., Icenogle J. P., Penaranda S., Bankamp B., Maher K., Chen M. H., Tong S., Tamin A., Lowe L., Frace M., DeRisi J. L., Chen Q., Wang D., Erdman D. D., Peret T. C., Burns C., Ksiazek T. G., Rollin P. E., Sanchez A., Liffick S., Holloway B., Limor J., McCaustland K., Olsen-Rasmussen M., Fouchier R., Gunther S., Osterhaus A. D., Drosten C., Pallansch M. A., Anderson L. J., Bellini W. J. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science (2003) 300:1394–1399Crossref, Google Scholar
• Rowe C. L., Fleming J. O., Nathan M. J., Sgro J. Y., Palmenberg A. C., Baker S. C. Generation of coronavirus spike deletion variants by high-frequency recombination at regions of predicted RNA secondary structure. J. Virology (1997) 71:6183–6190Crossref, Google Scholar
• Ruan Y. J., Wei C. L., Ling A. E., Vega V. B., Thoreau H., Su S. T., Chia J. M., Ng P., Chiu K. P., Lim L., Zhang T., Chan K. P., Oon L. E., Ng M. L., Leo S. Y., Ng L. F. P., Ren E. C., Stanton L. W., Long P. M., Liu E. T. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet (2003) 361:1779–1785Crossref, Google Scholar
• Schbath S., Prum B., de Turckheim E. Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comput. Biol. (1995) 2:417–437Crossref, Google Scholar
• Waterman M. S.Introduction to Computational Biology (1995) (Chapman & Hall, New York) Crossref, Google Scholar
• Worobey M., Holmes E. C. Evolutionary aspects of recombination in RNA viruses. J. General Virology (1999) 80:2535–2543Crossref, Google Scholar
• Yu X. J., Luo C., Lin J. C., Hao P., He Y. Y., Guo Z. M., Qin L., Su J., Liu B. S., Huang Y., Nan P., Li C. S., Xiong B., Luo X. M., Zhao G. P., Pei G., Chen K. X., Shen X., Shen J. H., Zou J. P., He W. Z., Shi T. L., Zhong Y., Jiang H. L., Li Y. X. Putative hAPN receptor binding sites in SARS-CoV spike protein. Acta Pharmacologica Sinica (2003) 24:481–488Google Scholar