Abstract
The BioTools Suite is a set of three comprehensive, platform-independent software packages (PepTool, GeneTool, and ChromaTool) developed for sequence assembly and analysis. In addition to supporting a large number of standard bioinformatics functions, these programs also incorporate a number of useful innovations including uniform graphical-user interface (GUI) design, direct internet connectivity, a novel approach to feature annotation, and a variety of enhanced algorithms for large scale proteome and genome analysis. This article describes the key features, recent changes, and general operation of all three programs.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Wishart, D. S., Boyko, R. F., Willard, L., et al. (1994) SEQSEE: a comprehensive programs suite for protein sequence analysis. Comput. Applic. Biosci. 10, 121–132.
Wishart, D. S. Boyko, R. F., and Sykes, B. D. (1994) Constrained multiple equence alignment using XALIGN. Comput. Applic. Biosci. 10, 687,688.
Wishart, D. S., Fortin, S., Woloschuk, D. R., et al. (1997) A platform-independent graphical user interface for SEQSEE and XALIGN. Comput. Applic. Biosci. 13, 561,562.
Wishart, D. S., Stothard, P., and Van Domselaar, G. H. (2000) PepTool and GeneTool: platform-independent tools for biological sequence analysis. Meth. Mol. Biol. 132, 93–113.
Basham, B. (1999) Protein structure at your desk. Science 283, 1132.
Nishimura, D. (1999) DNA analysis: new kid on the block. Science 285, 355,356.
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. 25, 3389–3402.
Hooper, P. M. (1999) Reference point logistic classification. J. Class. 16, 91–116.
Chou, P. Y. and Fasman, G. D. (1978) Empirical predictions of protein conformation. Ann. Rev. Biochem. 47, 251–276.
Garnier, J., Osguthorpe, D. J., and Robson, B. (1978) Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120, 97–120.
Klein, P., Kanehisa, M., and DeLisi, D. (1985) The detection and classification of membrane-spanning proteins. Biochim. Biophys. Acta 815, 468–476.
Nakamura, Y., Gojobori, T., and Ikemura, T. (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28, 292.
Hooper, P. M., Zhang, H., and Wishart, D. S. (2000) Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment. Bioinformatics 16, 425–438.
Burset, M. and Guigo, R. (1996) Evaluation of gene structure prediction programs. Genomics 34, 353–367.
Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94.
Snyder, E. E. and Stormo, G. D. (1995) Identification of protein coding regions in genomic DNA. J. Mol. Biol. 248, 1–18.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Wishart, D.S., Fortin, S. The BioTools Suite. Mol Biotechnol 19, 59–77 (2001). https://doi.org/10.1385/MB:19:1:059
Issue Date:
DOI: https://doi.org/10.1385/MB:19:1:059