Multi-Harmony: detecting functional specificity from sequence alignment

Research output: Contribution to JournalArticleAcademicpeer-review

113 Downloads (Pure)

Abstract

Many protein families contain sub-families with functional specialization, such as binding different ligands or being involved in different protein-protein interactions. A small number of amino acids generally determine functional specificity. The identification of these residues can aid the understanding of protein function and help finding targets for experimental analysis. Here, we present multi-Harmony, an interactive web sever for detecting sub-type-specific sites in proteins starting from a multiple sequence alignment. Combining our Sequence Harmony (SH) and multi-Relief (mR) methods in one web server allows simultaneous analysis and comparison of specificity residues; furthermore, both methods have been significantly improved and extended. SH has been extended to cope with more than two sub-groups. mR has been changed from a sampling implementation to a deterministic one, making it more consistent and user friendly. For both methods Z-scores are reported. The multi-Harmony web server produces a dynamic output page, which includes interactive connections to the Jalview and Jmol applets, thereby allowing interactive analysis of the results. Multi-Harmony is available at http://www.ibi.vu.nl/ programs/shmrwww.

Original languageEnglish
Pages (from-to)W35-40
JournalNucleic Acids Research
Volume38
Issue numberWeb Server issue
DOIs
Publication statusPublished - Jul 2010

Keywords

  • Algorithms
  • Internet
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Smad Proteins
  • Software
  • Journal Article
  • Research Support, Non-U.S. Gov't

Fingerprint

Dive into the research topics of 'Multi-Harmony: detecting functional specificity from sequence alignment'. Together they form a unique fingerprint.

Cite this