Detecting Distant Homology With Meta-BASIC

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W576-81. doi: 10.1093/nar/gkh370.

Abstract

Meta-BASIC (http://basic.bioinfo.pl) is a novel sensitive approach for recognition of distant similarity between proteins based on consensus alignments of meta profiles. Specifically, Meta-BASIC compares sequence profiles combined with predicted secondary structure by utilizing several scoring systems and alignment algorithms. In our benchmarking tests, Meta-BASIC outperforms many individual servers, including fold recognition servers, and it can compete with meta predictors that base their strength on the structural comparison of models. In addition, Meta-BASIC, which enables detection of very distant relationships even if the tertiary structure for the reference protein is not known, has a high-throughput capability. This new method is applied to 860 PfamA protein families with unknown function (DUF) and provides many novel structure-functional assignments available on-line at http://basic.bioinfo.pl/duf.pl. Detailed discussion is provided for two of the most interesting assignments. DUF271 and DUF431 are predicted to be a nucleotide-diphospho-sugar transferase and an alpha/beta-knot SAM-dependent RNA methyltransferase, respectively.

Publication types

  • Comparative Study
  • Evaluation Study

MeSH terms

  • Algorithms
  • Glycosyltransferases / chemistry
  • Glycosyltransferases / classification
  • Internet
  • Models, Molecular
  • Protein Structure, Secondary
  • Proteins / chemistry
  • Proteins / classification
  • Proteins / physiology
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Sequence Homology, Amino Acid
  • Software*
  • Structural Homology, Protein*
  • tRNA Methyltransferases / chemistry
  • tRNA Methyltransferases / classification

Substances

  • Proteins
  • tRNA Methyltransferases
  • Glycosyltransferases