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An Introduction to BioPerl

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 406))

Summary

The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record.

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Reference

  1. Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G., Korf, I., Lapp, H., Lehvaslaiho, H., Matsalla, C., Mungall, C. J., Osborne, B. I., Pocock, M. R., Schattner, P., Senger, M., Stein, L. D., Stupka, E., Wilkinson, M. D., and Birney, E. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12, 1611–18.

    Article  CAS  PubMed  Google Scholar 

  2. Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L., Durbin, R., and Ashburner, M. (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol 6, R44.

    Article  PubMed  Google Scholar 

  3. Stein, L. D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., and Lewis, S. (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12, 1599–610.

    Article  CAS  PubMed  Google Scholar 

  4. Altschul, S. F., Madden, T. L., Schaffer, 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. Nucleic Acids Res 25, 3389–402.

    Article  CAS  PubMed  Google Scholar 

  5. Pearson, W. R., and Lipman, D. J. (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85, 2444–48.

    Article  CAS  PubMed  Google Scholar 

  6. Eddy, S. R. (1998) Profile hidden Markov models. Bioinformatics 14, 755–63.

    Article  CAS  PubMed  Google Scholar 

  7. Kent, W. J. (2002) BLAT—the BLAST-like alignment tool. Genome Res 12, 656–64.

    CAS  PubMed  Google Scholar 

  8. Burge, C., and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268, 78–94.

    Article  CAS  PubMed  Google Scholar 

  9. Birney, E., Clamp, M., and Durbin, R. (2004) GeneWise and Genomewise. Genome Res 14, 988–95.

    Article  CAS  PubMed  Google Scholar 

  10. Parra, G., Blanco, E., and Guigo, R. (2000) GeneID in Drosophila. Genome Res 10, 511–15.

    Article  CAS  PubMed  Google Scholar 

  11. Borodovsky, M., and McIninch, J. (1993) Recognition of genes in DNA sequence with ambiguities. Biosystems 30, 161–71.

    Article  CAS  PubMed  Google Scholar 

  12. Delcher, A. L., Harmon, D., Kasif, S., White, O., and Salzberg, S. L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27, 4636–41.

    Article  CAS  PubMed  Google Scholar 

  13. Iseli, C., Jongeneel, C. V., and Bucher, P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol, 7, 138–48.

    Google Scholar 

  14. Zhang, M. Q. (1997) Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc Natl Acad Sci USA 94, 565–68.

    Article  CAS  PubMed  Google Scholar 

  15. Rozen, S., and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132, 365–86.

    CAS  PubMed  Google Scholar 

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© 2007 Humana Press Inc.

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Stajich, J.E. (2007). An Introduction to BioPerl. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology™, vol 406. Humana Press. https://doi.org/10.1007/978-1-59745-535-0_26

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  • DOI: https://doi.org/10.1007/978-1-59745-535-0_26

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-653-5

  • Online ISBN: 978-1-59745-535-0

  • eBook Packages: Springer Protocols

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