Detecting distant homology with Meta-BASIC

Krzysztof Ginalski, Marcin von Grotthuss, Nick V. Grishin, Leszek Rychlewski

Research output: Contribution to journalArticle

98 Scopus citations

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 α/β-knot SAM-dependent RNA methyltransferase, respectively.

Original languageEnglish (US)
Pages (from-to)W576-W581
JournalNucleic acids research
Volume32
Issue numberWEB SERVER ISS.
DOIs
StatePublished - Jul 1 2004

ASJC Scopus subject areas

  • Genetics

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    Ginalski, K., von Grotthuss, M., Grishin, N. V., & Rychlewski, L. (2004). Detecting distant homology with Meta-BASIC. Nucleic acids research, 32(WEB SERVER ISS.), W576-W581. https://doi.org/10.1093/nar/gkh370