Conservation, Evolutionary: Difference between revisions
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Eric Martz (talk | contribs) →The ConSurf-DB Mechanism: describing ConSurf-DB Mechanism |
Eric Martz (talk | contribs) →The ConSurf-DB Mechanism: describing ConSurf-DB Mechanism |
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The ConSurf DataBase server, [http://consurfdb.tau.ac.il ConSurf-DB]<ref name="consurfdb">PMID: 18971256</ref>, pre-calculates conservation levels for each amino acid in every protein chain in the [[Protein Data Bank]]. It went into service in 2008. Each chain is processed as follows. | The ConSurf DataBase server, [http://consurfdb.tau.ac.il ConSurf-DB]<ref name="consurfdb">PMID: 18971256</ref>, pre-calculates conservation levels for each amino acid in every protein chain in the [[Protein Data Bank]]. It went into service in 2008. Each chain is processed as follows. | ||
#The amino acid sequence of each protein chain is submitted to PSI-BLAST<ref>PSI-BLAST (Position Specific Iteration-BLAST) is an extension of the Basic Local Alignment Search Tool (BLAST) that is more sensitive at finding distantly related sequences. See [http://en.wikipedia.org/wiki/PSI-BLAST PSI-BLAST at Wikipedia] and [http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/psi1.html PSI-BLAST at NCBI].</ref> for collection of related sequences. | #The amino acid sequence of each protein chain is submitted to PSI-BLAST<ref>PSI-BLAST (Position Specific Iteration-BLAST) is an extension of the Basic Local Alignment Search Tool (BLAST) that is more sensitive at finding distantly related sequences. See [http://en.wikipedia.org/wiki/PSI-BLAST PSI-BLAST at Wikipedia] and [http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/psi1.html PSI-BLAST at NCBI].</ref> for collection of related sequences. Chains shorter than 30 amino acids are not processed because they do not contain enough information for reliable phylogenetic tree construction. Non-standard residues are converted to the closest standard amino acids. Chains with more than 15% non-standard residues are not processed. | ||
# The sequences gathered with PSI-BLAST are then filtered (see below) using a scheme that attempts a balance between limiting the sequences to close homologues, and including distant sequences that do not share structure or function. | # The sequences gathered with PSI-BLAST are then filtered (see below) using a scheme that attempts a balance between limiting the sequences to close homologues, and including distant sequences that do not share structure or function. | ||
#The filtered sequence set is multiply aligned with [http://www.drive5.com/muscle/ MUSCLE] (a multiple sequence alignment algorithm that out-performs CLUSTALW). | #The filtered sequence set is multiply aligned with [http://www.drive5.com/muscle/ MUSCLE] (a multiple sequence alignment algorithm that out-performs CLUSTALW). | ||
