Conservation, Evolutionary: Difference between revisions
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===INTREPID=== | ===INTREPID=== | ||
"[http://phylogenomics.berkeley.edu/INTREPID/index.html INTREPID] is an information-theoretic approach for functional site identification that exploits the information in large diverse multiple sequence alignments. INTREPID gathers homologs for a sequence using PSI-BLAST and estimates a phylogenetic tree. It then uses Jensen-Shannon divergence to measure the information for each position in the sequence at each subtree node encountered on a traversal of the phylogeny, tracing a path from the root to the leaf corresponding to the sequence of interest. Positions that are conserved across the entire family receive stronger scores than those that only become conserved within more closely related subgroups. This tree traversal produces a phylogenomic conservation score for each position in the MSA. INTREPID uses information from sequence only, and can thus be used when knowledge of structure is not available." | "[http://phylogenomics.berkeley.edu/INTREPID/index.html INTREPID] is an information-theoretic approach for functional site identification that exploits the information in large diverse multiple sequence alignments. INTREPID gathers homologs for a sequence using PSI-BLAST and estimates a phylogenetic tree. It then uses Jensen-Shannon divergence to measure the information for each position in the sequence at each subtree node encountered on a traversal of the phylogeny, tracing a path from the root to the leaf corresponding to the sequence of interest. Positions that are conserved across the entire family receive stronger scores than those that only become conserved within more closely related subgroups. This tree traversal produces a phylogenomic conservation score for each position in the MSA. INTREPID uses information from sequence only, and can thus be used when knowledge of structure is not available." (Quoted from the [http://phylogenomics.berkeley.edu/INTREPID/index.html INTREPID website].) | ||
INTREPID accepts a protein chain sequence as input. It offers to color conserved residues on 3D protein structures in Jmol. The 3D structures are obtained (when available) from the [[Protein Data Bank]] by sequence alignment searching, and users may choose from a menu of hits. | INTREPID accepts a protein chain sequence as input. It offers to color conserved residues on 3D protein structures in Jmol. The 3D structures are obtained (when available) from the [[Protein Data Bank]] by sequence alignment searching, and users may choose from a menu of hits. | ||
