Advertisement

Managing Sequencing Projects in the GAP4 Environment

  • Rodger Staden
  • David P. Judge
  • James K. Bonfield
Chapter

Abstract

Methods for managing large scale sequencing projects are available through the use of our GAP4 package and the applications to which it can link are described. This main assembly and editing program, also provides a graphical user interface to the assembly engines: CAP3, FAKII, and PHRAP. Because of the diversity of working practices in the large number of laboratories where the package is used, these methods are very flexible and are readily tailored to suit local needs. For example, the Sanger Centre in the UK and the Whitehead Institute in the United States have both made major contributions to the human genome project using the package in different ways. The manual for the current (2001.0) version of the package is over 500 pages when printed, so this chapter is a brief overview of some of its most important components. We have tried to show a logical route through the methods in the package: pre-processing, assembly, contig1 ordering using read-pairs, contig joining using sequence comparison, assembly checking, automated experiment suggestions for extending contigs and solving problems, and ending with editing and consensus file generation. Before this overview, two important aspects of the package are outlined: the file formats used, the displays and the powerful user interface of GAP4. The package runs on UNIX and Microsoft Windows platforms and is entirely free to academic users, and can be downloaded from Website: http://www.mrc-lmb.cam.ac.uk/pubseq.

Keywords

Hide Data Consensus Algorithm Output Window Sequencing Instrument Experiment File 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Suggested Readings

Sequence Assembly

  1. Bonfield, J. K., Smith, K. F., and Staden, R. (1995) A new DNA sequence assembly program, Nucleic Acids Res. 23, 4992–4999.PubMedCrossRefGoogle Scholar
  2. Green, P. H. (1997) Personal communication.Google Scholar
  3. Huang, X. and Madden, A. (1999) CAP3: A DNA Sequence Assembly Program, Genome Res. 9, 868–877.PubMedCrossRefGoogle Scholar
  4. Myers, E. W., Jain, M., and Larson, S. (1996) Internal report, University of Arizona, Tucson, AZ.Google Scholar
  5. Staden, R. (1980) A new computer method for the storage and manipulation of DNA gel reading data, Nucleic Acids Res. 8, 3673–3694.PubMedCrossRefGoogle Scholar

File Formats: SCF, ZTR, Experiment, Fasta Files, and the GAP4 Database

  1. Bonfield, J. K. and Staden, R. (2002) ZTR: A new format for DNA sequence trace data, Bioinformatics 18(1), 3–10.PubMedCrossRefGoogle Scholar
  2. Bonfield, J. K. and Staden, R. (1996) Experiment files and their application during large-scale sequencing projects, DNA Sequence 6, 109–117.PubMedGoogle Scholar
  3. Dear, S. and Staden, R. (1992) A standard file format for data from DNA sequencing instruments, DNA Sequence 3, 107–110.PubMedGoogle Scholar
  4. Pearson, W. R. (1994) Using the FASTA Program to Search Protein and DNA Sequence Databases, in: Methods in Molecular Biology, (Griffin, A. M. and Griffin, H. G., eds.), vol. 25, Humana Press, Totowa, NJ, pp. 365–389.Google Scholar

Tool Kits

  1. Free Software Foundation, 675 Mass Avenue, Cambridge, MA 02139.Google Scholar
  2. Ousterhout, J. K. (1994) Tcl and the Tk toolkit, Addison-Wesley Publishing Company, Reading, MA.Google Scholar

Other Programs

  1. Haas, S., Vingron, M., Poustka, A., and Wiemann, S. (1998) Primer design for large scale sequencing, Nucleic Acids Res. 26, 3006–3012.PubMedCrossRefGoogle Scholar
  2. Bonfield, J. K., Rada, C., and Staden, R. (1998) Automated detection of point mutations using flourescent sequence trace subtraction, Nucleic Acids Res. 26, 3404–3409.PubMedCrossRefGoogle Scholar
  3. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool, J. Mol. Biol. 215, 403–410.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2003

Authors and Affiliations

  • Rodger Staden
  • David P. Judge
  • James K. Bonfield

There are no affiliations available

Personalised recommendations