ArticleNucleic acids research2007
Sequence harmony: detecting functional specificity from alignments.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Genome-Wide Identification and Hormone-Induced Expression Analysis of the Anthocyanidin Reductase Gene Family in Sainfoin (International journal of molecular sciences · 2025Article
- Article
- Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications.Frontiers in bioengineering and biotechnology · 2021Article
- Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl.Frontiers in molecular biosciences · 2021Article
- Recurrent sequence evolution after independent gene duplication.BMC evolutionary biology · 2020Article
- Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants.Plant molecular biology · 2018Article
- Exploiting sequence and stability information for directing nanobody stability engineering.Biochimica et biophysica acta. General subjects · 2017Article
- Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes.BMC evolutionary biology · 2017Article
- Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases.The Journal of biological chemistry · 2017Article
- The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS.PloS one · 2016Article
- HIV-1 replication fitness of HLA-B*57/58:01 CTL escape variants is restored by the accumulation of compensatory mutations in gag.PloS one · 2013Article
- SPEER-SERVER: a web server for prediction of protein specificity determining sites.Nucleic acids research · 2012Article
- Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.BMC bioinformatics · 2012Article
- Structure based hypothesis of a mitochondrial ribosome rescue mechanism.Biology direct · 2012Article
- Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms.Statistical applications in genetics and molecular biology · 2011Article
- Mining bacterial genomes for novel arylesterase activity.Microbial biotechnology · 2010Article
- An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.Algorithms for molecular biology : AMB · 2010Article
- Multi-Harmony: detecting functional specificity from sequence alignment.Nucleic acids research · 2010Article
- webPRC: the Profile Comparer for alignment-based searching of public domain databases.Nucleic acids research · 2009Article
- INTREPID: a web server for prediction of functionally important residues by evolutionary analysis.Nucleic acids research · 2009Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The SH web server allows a quick selection of subtype specific sites from a multiple alignment given a subfamily grouping. In addition, it allows the predicted sites to be directly mapped onto a protein structure and displayed. We demonstrate the use of the SH server using the family of plant mitochondrial alternative oxidases (AOX). In addition, we illustrate the usefulness of combining sequence and structural information by showing that the predicted sites are clustered into a few distinct regions in an AOX homology model. The SH web server can be accessed at www.ibi.vu.nl/programs/seqharmwww.
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