Conservation, Evolutionary: Difference between revisions
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===INTREPID=== | ===INTREPID=== | ||
In 2024, the INTREPID Server, formerly at the University of California, Berkeley, appears to be unavailable. | |||
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"[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].) | "[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].) | ||
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Evidence is provided that INTREPID out-performs ConSurf for predicting catalytic residues. | Evidence is provided that INTREPID out-performs ConSurf for predicting catalytic residues. | ||
Unlike ConSurf, INTREPID does not identify the [[#Locating Variable Patches|most variable residues]] in addition to the [[#Locating Conserved Patches|most conserved]]. | Unlike ConSurf, INTREPID does not identify the [[#Locating Variable Patches|most variable residues]] in addition to the [[#Locating Conserved Patches|most conserved]]. --> | ||
===xProtCAS=== | ===xProtCAS=== | ||
