Ion Channel Phylogenomic Explorer v. 2.0.   24 July 2008: 55 families; 432 Hidden Markov Models (family and subfamily).

We combine evolutionary tree construction with structure analysis to reconstruct the phylogeny of ion channel proteins and provide subfamily classifications. The molecular evolution of these complex proteins involves gene duplication and domain shuffling, to produce a vast and challenging superfamily of biological macromolecules.

This work is funded by grant number R01 HG002769 from the National Human Genome Research Institute of the NIH.

Please cite the following paper in references to this resource : Sjölander, K., "Phylogenomic inference of protein molecular function: advances and challenges," Bioinformatics 2004 (20)2:170-179. Oxford University Press access.

Protein Search

Submit sequences for classification against the HMM library. This library is designed to help biologists do the following:

• Predict molecular function by phylogenomic analysis, using the phylogenetic tree for the family.
• Classify novel sequences to functional subtypes, using the subfamily HMMs for the family.
• Predict specificity positions, using the alignment analysis plots for each family.

Each "book" in the HMM library corresponds roughly to a (whole-chain) protein family or domain, and contains the following data (generally downloadable, in different formats):

• A cluster of homologs, typically from many species
• One or more phylogenetic trees.
• A decomposition of the tree into subtrees, to identify functional subfamilies.
• A multiple sequence alignment for the family, as well as for individual subfamilies.
• GO (Gene Ontology) annotations and evidence codes.
• Other annotations and experimental data.
• Hyperlinks to papers and online resources.
• An analysis of the family's multiple sequence alignment using the subfamily decomposition to predict specificity positions defining the individual subtypes.
• A predicted structure, including construction of comparative models for some families.
• A predicted cellular localization (i.e., membrane-localized, secreted, cytoplasmic, nuclear, etc.