Skip to main content

Multiple Sequence Alignment and Analysis

The SeqLab Interface: A Practical Guide

  • Chapter
  • 1003 Accesses

Abstract

SeqLab is based on Steve Smith’ s (1994) GDE (Genetic Data Environment) and is a part of Accelrys’ Genetics Computer Group Wisconsin Package. This comprehensive package of sequence analysis programs is used worldwide and is an industry-standard. The GCG Package only operates runs on server computers running the UNIX operating system but it can be accessed from any networked terminal. Specialized X-servergraphics communications software is required to display GCG’s SeqLab GUI. X server emulation software needs to be installed separately on personal style Microsoft Windows/Intel or Macintosh machines but genuine X Windowing comes standard with most UNIX operating systems. Wintelmachines are often set up with either XWin32 or eXceed to provide this function; Macintoshes are often loaded with either MacX or eXodus software.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   189.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Suggested Reading

SeqLab and Multiple Sequence Reading

  • Etzold, T. and Argos, P. (1993) SRS—an indexing and retrieval tool for flat file data libraries, Comp. Appl. Biosc. 9, 49–57.

    PubMed  CAS  Google Scholar 

  • Genetics Computer Group (GCG), a part of Accelrys Inc., a subsidiary of Pharmacopeia Inc. (©1982–2002) Program Manual for the Wisconsin Package, Version 10.2, Madison, WI. (seeWebsite: http://www.accelrys.com/products/gcg-wisconsin-package)

  • Gilbert, D. G. (1993 [C release] and 1999 [Java release]) ReadSeq, Bioinformatics Group, Biology Department, Indiana University, Bloomington, IN. (For public domain software, seeWebsite: http://www.iubio.bio.indiana.edu/soft/ molbio/readseq)

  • National Center for Biotechnology Information (NCBI) Entrez, National Library of Medicine, National Institutes of Health, Bethesda, MD. (For public domain software, seeWebsite: http://www.ncbi.nlm.nih.gov/Entrez)

  • Smith, S. W., Overbeek, R., Woese, C. R., Gilbert, W., and Gillevet, P. M. (1994) The Genetic Data Environment, an expandable GUI for multiple sequence analysis, Comp. Appl. Biosci. 10, 671–675.

    PubMed  CAS  Google Scholar 

  • von Heijne, G. (1987) Sequence Analysis in Molecular Biology; Treasure Trove or Trivial Pursuit, Academic Press, San Diego, CA.

    Google Scholar 

Similarity Searching

  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic Local Alignment Tool, J. Mol. Biol. 215, 403–410.

    PubMed  CAS  Google Scholar 

  • 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, 3389–3402.

    Article  PubMed  CAS  Google Scholar 

  • Pearson, W. R. and Lipman, D. J. (1988) Improved tools for biological sequence analysis, Proc. Natl. Acad. Sci. USA 85, 2444–2448.

    Article  PubMed  CAS  Google Scholar 

  • Pearson, W. B. (1998) Empirical statistical estimates for sequence similarity searches, J. Mol. Biol. 276, 71–84.

    Article  PubMed  CAS  Google Scholar 

Indentifying Motifs

  • Bailey, T. L. and Elkan, C., (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers, in: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, CA, pp. 28–36.

    Google Scholar 

  • Bailey, T. L. and Gribskov, M. (1998) Combining evidence using p-values: application to sequence homology searches, Bioinformatics 14, 48–54.

    Article  PubMed  CAS  Google Scholar 

  • Bairoch, A. (1992) PROSITE: A dictionary of sites and patterns in proteins, Nucleic Acids Res. 20, 2013–2018.

    Article  PubMed  CAS  Google Scholar 

  • Gribskov, M., Luethy, R., and Eisenberg, D. (1989) Profile analysis, in: Methods in Enzymology, vol. 183, Academic Press, San Diego, CA, pp. 146–159.

    Google Scholar 

  • Gribskov, M., McLachlan, M., and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins, Proc. Natl. Acad. Sciences USA 84, 4355–4358.

    Google Scholar 

The Scoring Matrix

  • Henikoff, S. and Henikoff, J. G. (1992) Amino acid substitution matrices from protein blocks, Proc. Natl. Acad. Sci. USA 89, 10,915–10,919.

    Article  Google Scholar 

  • Schwartz, R. M. and Dayhoff, M. O. (1979) Matrices for detecting distant relationships, in: Atlas of Protein Sequences and Structure, vol. 5 (Dayhoff, M. O., ed.), National Biomedical Research Foundation, Washington, DC, pp. 353–358.

    Google Scholar 

Phylogenetics

  • Dobzhansky, T., Ayala, F. J., Stebbins, G. L., and Valentine, J. W. (1977) Evolution, W. H. Freeman and Co., San Francisco, CA. The source of the original 1973 quote is obscure though it has been cited as being transcribed from the American Biology Teacher (1973) 35, 125–129.

    Article  Google Scholar 

  • Felsenstein, J. (1980–2001) Phylogeny Inference Package (PHYLIP) version 3.5+, Department of Genetics, University of Washington, Seattle, WA. (For public domain software seeWebsite: http://www.evolution.genetics.washington.edu/phylip.html)

  • Feng, D. F. and Doolittle, R. F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees, J. Mol. Evol. 25, 351–360

    Article  PubMed  CAS  Google Scholar 

  • Sogin, M. L., Morrison, H. G., Hinkle, G., and Silberman, J. D. (1996) Ancestral relationships of the major eukaryotic lineages, Microbiolgia Sem. 12, 17–28.

    CAS  Google Scholar 

  • Swofford, D. L. (1989–2001) PAUP* (Phylogenetic Analysis Using Parsimony and other methods), version 4.0+, Illinois Natural History Survey (1994), Smithsonian Institution (1998), Florida State University (2001). (seeWebsite: http://paup. csit.fsu.edu) Distributed through Sinaeur Associates, Inc., Sunderland, MA. (seeWebsite: http://www.sinauer.com/)

Hidden Markow Models

Download references

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer Science+Business Media New York

About this chapter

Cite this chapter

Thompson, S.M. (2003). Multiple Sequence Alignment and Analysis. In: Krawetz, S.A., Womble, D.D. (eds) Introduction to Bioinformatics. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59259-335-4_33

Download citation

  • DOI: https://doi.org/10.1007/978-1-59259-335-4_33

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-58829-241-4

  • Online ISBN: 978-1-59259-335-4

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics