Playing with blocks: some pitfalls of forcing multiple alignments - PubMed

Affiliations

• PMID: 1669287

Review

Playing with blocks: some pitfalls of forcing multiple alignments

S Henikoff. New Biol. 1991 Dec.

Abstract

Block alignments of multiple amino acid sequences are useful representations of regions thought to share common ancestry and function. Often the block alignments are motivated by the expectation that a protein of interest is similar in function to members of a family of proteins. However, when alignments are forced by using ad hoc methods, it is often difficult to decide whether the proposed relationship is valid. Visual examination can be deceptive, especially when alignments are not carried out in the context of controls subjected to similar procedures. Even computer-aided methods can be misleading when biases are introduced. To illustrate some of the problems that can arise, a few examples from the literature are analyzed. It is concluded that when standard methods fail to find an interesting block alignment unaided by human intervention, then the result should be regarded with caution.

Similar articles

• Understanding structural relationships in proteins of unsolved three-dimensional structure.

  Burbaum JJ, Starzyk RM, Schimmel P. Burbaum JJ, et al. Proteins. 1990;7(2):99-111. doi: 10.1002/prot.340070202. Proteins. 1990. PMID: 2183216 Review.

• Structure-based phylogeny of class IIa tRNA synthetases in relation to an unusual biochemistry.

  Ribas de Pouplana L, Brown JR, Schimmel P. Ribas de Pouplana L, et al. J Mol Evol. 2001 Oct-Nov;53(4-5):261-8. doi: 10.1007/s002390010216. J Mol Evol. 2001. PMID: 11675586

• The Escherichia coli YadB gene product reveals a novel aminoacyl-tRNA synthetase like activity.

  Campanacci V, Dubois DY, Becker HD, Kern D, Spinelli S, Valencia C, Pagot F, Salomoni A, Grisel S, Vincentelli R, Bignon C, Lapointe J, Giegé R, Cambillau C. Campanacci V, et al. J Mol Biol. 2004 Mar 19;337(2):273-83. doi: 10.1016/j.jmb.2004.01.027. J Mol Biol. 2004. PMID: 15003446

• Protein sequence comparisons: searching databases and aligning sequences.

  Doolittle RF. Doolittle RF. Curr Opin Biotechnol. 1994 Feb;5(1):24-8. doi: 10.1016/s0958-1669(05)80065-5. Curr Opin Biotechnol. 1994. PMID: 7764639 Review.

Cited by

• Consensus inverted terminal repeat sequence of Paramecium IESs: resemblance to termini of Tc1-related and Euplotes Tec transposons.

  Klobutcher LA, Herrick G. Klobutcher LA, et al. Nucleic Acids Res. 1995 Jun 11;23(11):2006-13. doi: 10.1093/nar/23.11.2006. Nucleic Acids Res. 1995. PMID: 7596830 Free PMC article.

• SAGA: sequence alignment by genetic algorithm.

  Notredame C, Higgins DG. Notredame C, et al. Nucleic Acids Res. 1996 Apr 15;24(8):1515-24. doi: 10.1093/nar/24.8.1515. Nucleic Acids Res. 1996. PMID: 8628686 Free PMC article.

• Bacterial signal transduction network in a genomic perspective.

  Galperin MY. Galperin MY. Environ Microbiol. 2004 Jun;6(6):552-67. doi: 10.1111/j.1462-2920.2004.00633.x. Environ Microbiol. 2004. PMID: 15142243 Free PMC article. Review.

• Sequence analysis of the AAA protein family.

  Beyer A. Beyer A. Protein Sci. 1997 Oct;6(10):2043-58. doi: 10.1002/pro.5560061001. Protein Sci. 1997. PMID: 9336829 Free PMC article. Review.

Publication types

MeSH terms

Substances