Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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COCAW: A Genome-wide Pattern Search System for Designing Microbial Probes

  • Ryu, Seung-Hee (Visual and Biomedical Computing Lab., Pusan National University) ;
  • Park, Kie-Jung (PNU SuperComputing Center, Pusan National University) ;
  • Lee, Do-Hoon (Visual and Biomedical Computing Lab., Pusan National University) ;
  • Kim, Cheol-Min (School of Medicine, Pusan National University)
  • Published : 2009.09.30
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Abstract

A few bioinformatics tools have been used to find out conserved regions as probes. We have developed a system based on a heuristic method with web interfaces to find out conserved regions against microbial genomes. The system runs in real time by using relative entropy in limited narrow regions and detecting similar regions between pair regions with local alignment. The system could be useful to find out conserved regions as genome-wide scale.

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References

  1. Andreson, R., Reppo, E., Kaplinski, L., and Remm, M. (2006). GENOMEMASKER package for designing unique genomic PCR primers. BMC Bioinform. 7, 172 https://doi.org/10.1186/1471-2105-7-172
  2. Altschul, S.F., Madden, T.L., Sch$\ddot{a}$ffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389-3402 https://doi.org/10.1093/nar/25.17.3389
  3. Boutros, R., Stokes, N., Bekaert, M., and Teeling, E.C. (2009). UniPrime2: a web service providing easier Universal Primer design. Nucl. Acids Res . 37, W209-213 https://doi.org/10.1093/nar/gkp269
  4. Boyce, R., Chilana, P., and Rose, T.M. (2009). iCODEHOP: a new interactive program for designing COnsensus DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. Nucl. Acids Res . 37, W222-228 https://doi.org/10.1093/nar/gkp379
  5. Kent, W.J. (2002). BLAT--the BLAST-like alignment tool. Genome Res . 12, 656-664 https://doi.org/10.1101/gr.229202
  6. Moro, C.V., Crouzet, O., Rasconi, S., Thouvenot, A., Coffe, G., Batisson, I., and Bohatier, J. (2009). New design strategy for development of specific primer sets for PCR-based detection of Chlorophyceae and Bacillariophyceae in environmental samples. Appl. Environ. Microbiol . 75, 5729-5733 https://doi.org/10.1128/AEM.00509-09
  7. Pearson, W.R. (1990), Rapid and sensitive sequence comparison with FASTP and FASTA, Methods Enzymol . 183, 63-98 https://doi.org/10.1016/0076-6879(90)83007-V
  8. Thompson, J.D., Gibson, T.J., and Higgins, D.G. (2002). Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinform. Chapter 2, Unit 2.3
  9. van Baren, M.J., and Heutink, P. (2004). The PCR suite. Bioinformatics . 20, 591-593 https://doi.org/10.1093/bioinformatics/btg473
  10. You, F.M., Huo, N., Gu, Y.Q., Luo, M.C., Ma, Y., Hane, D.,Lazo, G.R., Dvorak, J., and Anderson, O.D. (2008). BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinform . 9, 253 https://doi.org/10.1186/1471-2105-9-253