Abstract
The TIGR Assembler (TA) (1) is the sequence assembly program used in sequencing projects at The Institute for Genomic Research (TIGR). Development of the TA was based on the experience obtained in more than 20 sequencing projects completed at TIGR (see http://www.tigr.org). This extensive experience led to a sequence assembler that produces few misassemblies (2,3) and has been used successfully in whole-genome shotgun sequencing of prokaryotic and eukaryotic organisms, bacterial artificial chromosome-based sequencing of eukaryotic organisms, and expressed sequence tag assembly.
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
Sutton, G. G., White, O., Adams, M. D., and Kerlavage, A. R. (1995) TIGR Assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci. Technol. 1, 9–19.
Liang, F., Holt, I., Pertea, G., Karamycheva, S., Salzberg, S. L., and Quackenbush, J. (2000) An optimized protocol for analysis of EST sequences. Nucleic Acids Res. 28(18), 3657–3665.
Pevzner, P., Tang, H., and Waterman, M. S. (2001) A new approach to fragment assembly in DNA sequencing, in Proceedings of the Fifth Annual International Conference on Computational Biology (RECOMB). (Istrail, Lengauer, Pevzner, Sankoff, and Waterman, eds.), Association for Computing Machinery, Montreal, Canada. pp. 256–265.
Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185.
Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194.
Staden, R. (1979) A strategy of DNA sequencing employing computer programs. Nucleic Acids Res. 6(7), 2601–2610.
Tarhio, J. and Ukkonen, E. (1988) A greedy approximation algorithm for constructing shortest common superstrings. Theoret. Comput. Sci. 57, 131–145.
Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197.
Gribskov, M., McLachlan, A. D., and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84, 4355–4358.
Green, P. http://bozeman.mbt.washington.edu/phrap.docs/phrap.html.
Huang, X. (1996) An improved sequence assembly program. Genomics 33, 21–31.
Huang, X. and Madan, A. (1999) CAP3: a DNA sequence assembly program. Genome Res. 9(9), 867–877.
Pearson, W. R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183, 63–98.
Smith, S. W., Overbeek, R., Woese, C. R., Gilbert, W., and Gillevet, P. M. (1994) The genetic data environment and expandable GUI for multiple sequence analysis. Comput. Appl. Biosci. 10(6), 671–675.
Thierry-Mieg, J. and Durbin, R. (1992) ACEDB—a C. elegans database: syntactic definitions for the ACEDB data base manager, 1992 (http://www.acedb.org).
Gordon, D., Abajian, C., and Green, P. (1998) Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Pop, M., Kosack, D. (2004). Using the TIGR Assembler in Shotgun Sequencing Projects. In: Zhao, S., Stodolsky, M. (eds) Bacterial Artificial Chromosomes. Methods in Molecular Biology™, vol 255. Humana Press. https://doi.org/10.1385/1-59259-752-1:279
Download citation
DOI: https://doi.org/10.1385/1-59259-752-1:279
Publisher Name: Humana Press
Print ISBN: 978-0-89603-988-9
Online ISBN: 978-1-59259-752-9
eBook Packages: Springer Protocols