Abstract
Lasergene comprises eight applications, organized into functional units. A user with the full Lasergene system might employ the software as follows:
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Blattner, F. R., Plunket III, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., and Shao, Y. (1997) The complete genome sequence of Escherichia coli K12. Science 277, 1453–1462.
Burland, V., Daniels, D. L., Plunkett III, G., and Blattner, F. R. (1993) Genome sequencing on both strands: the Janus strategy. Nucleic Acids Res. 21, 3385–3390.
Allex, C. F., Baldwin, S. F., Shavlik, J. W., and Blattner, F. R. (1997) Increasing consensus accuracy in DNA fragment assemblies by incorporating fluorescent trace representations, in Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (Gaasterland, T., Karp, P., Karplus, K. Ouzounis, C., Sander, C., Valencia, A.), AAAI Press, Menlo Park, pp. 3–14.
Borodovsky, M. and McIninch, J. (1993) GeneMark: parallel gene recognition for both DNA strands. Comp. Chem. 17, 123–133.
Trifonov, E. N. and Sussman, J. L. (1980) The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA 77, 3816–3820.
Chou, P. Y. (1990) Prediction of protein structural classes from amino acid composition, in Prediction of Protein Structure and the Principles of Protein Conformation (Fasman, G. D., ed.), Plenum, New York, NY, pp. 549–586.
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.
Deléage, G. and Roux, B. (1987) An algorithm for protein secondary structure prediction based on class prediction. Protein Eng. 1, 289–294.
Parry, D. A. (1982) Coiled coils in α-helix-containing proteins: analysis of the residue types in the heptad repeat and the use of these data in the prediction of coiled coils in other proteins. Biosci. Rep. 2, 1017–1024.
Engelman, D. M., Steitz, T. A., and Goldman, A. (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem 15, 321–54.
Kyte, J. and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105–132.
Hopp, T. P. and Woods, K.R. (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl. Acad. Sci. USA 78, 3824–3828.
Eisenberg, D., Weiss, R. M., and Terwilliger, T. C. (1984) The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. USA 81, 140–144.
Bairoch, A., Bucher, P., and Hofmann, K. (1997) The PROSITE database, its status in 1997. Nucleic Acids Res. 25, 217–221.
Margalit, H., Spouge, J. L., Cornette, J. L., Cease, K. B., Delisi, C., and Berzofsky, J. A. (1987) Prediction of immunodominant helper T cell antigenic sites from the primary sequence. J. Immunol. 138, 2213–2229.
Jameson, B. A. and Wolf, H. (1988) The antigenic index: a novel algorithm for predicting antigenic determinants. Comp. Appl. Biosci. (now Bioinformatics) 4, 181–186.
Sette, A., Buus, S., Appella, E., Smith, J. A., Chesnut, R., Miles, C., Colon, S. M., and Grey, H. M. (1989) Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis. Proc. Natl. Acad. Sci. USA 86, 3296–3300.
Rothbard, J. B. and Taylor, W. R. (1988) A sequence pattern common to T cell epitopes. EMBO J. 7, 93–100.
Emini, E. A., Hughes, J., Perlow, D., and Boger, J. (1985) Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J. Virol. 55, 836–839.
Martinez, H. M. (1983) An efficient method for finding repeats in molecular sequences. Nucleic Acids Res. 11, 4629–4634.
Wilbur, W. J. and Lipman, D. J. (1983) Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl. Acad. Sci. USA 80, 726–730.
Lipman, D. J. and Pearson, W. R. (1985) Rapid and sensitive protein similarity searches. Science 227, 1435–1441.
Hein, J. (1990) Unified approach to alignment and phylogenies. Meth. Enzymol. 183, 626–645.
Higgins, D. G. and Sharp, P. M. (1989) Fast and sensitive multiple sequence alignments on a microcomputer. Comp. Appl. Biosci. (now Bioinformatics) 5, 151–153.
Pearson, W. R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Meth. Enzymol. 183, 63–98.
Bucher, P. and Bairoch, A. (1994) A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation, in Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology (Altman R., Brutlag D., Karp P., Lathrop R., Searls D., eds.), AAAI Press, Menlo Park, CA, pp. 53–61.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2000 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Burland, T.G. (2000). DNASTAR’s Lasergene Sequence Analysis Software. In: Misener, S., Krawetz, S.A. (eds) Bioinformatics Methods and Protocols. Methods in Molecular Biology™, vol 132. Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-192-2:71
Download citation
DOI: https://doi.org/10.1385/1-59259-192-2:71
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-0-89603-732-8
Online ISBN: 978-1-59259-192-3
eBook Packages: Springer Protocols