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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Reference
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.
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.
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.
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.
Pearson, W. R., and Lipman, D. J. (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85, 2444–48.
Eddy, S. R. (1998) Profile hidden Markov models. Bioinformatics 14, 755–63.
Kent, W. J. (2002) BLAT—the BLAST-like alignment tool. Genome Res 12, 656–64.
Burge, C., and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268, 78–94.
Birney, E., Clamp, M., and Durbin, R. (2004) GeneWise and Genomewise. Genome Res 14, 988–95.
Parra, G., Blanco, E., and Guigo, R. (2000) GeneID in Drosophila. Genome Res 10, 511–15.
Borodovsky, M., and McIninch, J. (1993) Recognition of genes in DNA sequence with ambiguities. Biosystems 30, 161–71.
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.
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.
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.
Rozen, S., and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132, 365–86.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this protocol
Cite this protocol
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
Download citation
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