Computer Corner
Iterated profile searches with PSI-BLAST—a tool for discovery in protein databases

https://doi.org/10.1016/S0968-0004(98)01298-5Get rights and content

Section snippets

Sequence profiles

Many functionally and evolutionarily important protein similarities are recognizable only through comparison of three-dimensional structures12, 13. When such structures are not available, patterns of conservation identified from the alignment of related sequences can aid the recognition of distant similarities. There is a large literature on the definition and construction of these patterns, which have been variously called motifs, profiles, position-specific score matrices, and Hidden Markov

The design of PSI-BLAST

Iterated profile search methods have led to biologically important observations but, for many years, were quite slow and generally did not provide precise means for evaluating the significance of their results. This limited their utility for systematic mining of the protein databases. The principal design goals in developing the Position-Specific Iterated BLAST (PSI-BLAST) program[4]were speed, simplicity and automatic operation. The procedure PSI-BLAST uses can be summarized in five steps.

  • 1.

A PSI-BLAST example

PSI-BLAST uncovers many protein relationships missed by single-pass database-search methods and has identified relationships that were previously detectable only from information about the three-dimensional structure of the proteins4, 22, 23. Here, we illustrate how to operate PSI-BLAST by using a comparison of proteins from thermophilic archaea and bacteria as an example[24]. We employed the WWW version of PSI-BLAST, which can be accessed at http://www.ncbi.nlm.nih.gov/BLAST.

A search is

Notes on using PSI-BLAST

The WWW version of PSI-BLAST requires the user to decide after each iteration whether to continue. In some respects, this is a limitation, but it has the advantage that the user can hand-pick the sequences used for each profile construction, regardless of E value, by checking boxes next to the sequences' descriptions (Fig. 1). A stand-alone version of PSI-BLAST (obtainable from NCBI at ftp://ncbi.nlm.nih.gov/blast/executables/) allows the user to run the program for a chosen number of

Conclusion

PSI-BLAST alters the database-searching landscape. Many important but subtle relationships that previously were detectable only by the fairly laborious application of several methods, or by structural comparison, can now be identified more easily. Although a PSI-BLAST search is easy to launch, the program increases rather than removes the need for expertise, because there is more to interpret.

PSI-BLAST has room for improvement. The profile-construction process is fairly naive, and increased

Acknowledgements

We thank the developers of PSI-BLAST, who include D. J. Lipman, T. L. Madden, W. Miller, A. A. Schäffer, J. Zhang and Z. Zhang. We also thank L. Aravind for his collaboration on the application of PSI-BLAST to the detection of subtle relationships among proteins.

First page preview

First page preview
Click to open first page preview

References (30)

  • S.F. Altschul

    J. Mol. Biol.

    (1990)
  • S.F. Altschul et al.

    Methods Enzymol.

    (1996)
  • T.F. Smith et al.

    J. Mol. Biol.

    (1981)
  • W.R. Pearson

    J. Mol. Biol.

    (1998)
  • L. Holm et al.

    Structure

    (1997)
  • T.S. Schneider et al.

    J. Mol. Biol.

    (1986)
  • M. Gribskov

    Gene

    (1992)
  • P. Bucher et al.

    Comput. Chem.

    (1996)
  • M. Huynen

    J. Mol. Biol.

    (1998)
  • J.C. Wootton et al.

    Methods Enzymol.

    (1996)
  • A. Lupas

    Methods Enzymol.

    (1996)
  • W.R. Pearson et al.

    Proc. Natl. Acad. Sci. U. S. A.

    (1988)
  • S.F. Altschul

    Nucleic Acids Res.

    (1997)
  • S. Karlin et al.

    Proc. Natl. Acad. Sci. U. S. A.

    (1990)
  • S. Karlin et al.

    Proc. Natl. Acad. Sci. U. S. A.

    (1993)
  • Cited by (0)

    View full text