ConSurfDB vs. ConSurf: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Timothy Gregory, Joel L. Sussman

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 # Filters the sequences, by default eliminating those redundant at 95% or higher identity with each other, and those with less than 35% sequence identity to the query sequence. These percentages are adjustable.
 #Optionally enables the user to manually select which sequences will be used, from a list with checkboxes. In particular, this enables users to limit the analysis to proteins having the same function as the protein of interest (see  [[#Limiting ConSurf Analysis to Proteins of a Single Function|above]]).
-# Does a multiple sequence alignment with MUSCLE. (Or you can upload your own MSA.)
+# Does a multiple sequence alignment with MAFFT. (Or you can choose a different algorithm or upload your own MSA.)
-# Constructs a phylogenetic tree. (Or you can upload your own.)
+# Constructs a phylogenetic tree using neighbor joining with ML distance. (Or you can choose a different algorithm or upload your own tree.)
-# Calculates a conservation score for each amino acid. Classifies the conservation scores into nine levels, and maps them to standard conservation level colors (see color key at the top of this page). Marks residues for which the conservation score confidence interval is too large, hence the conservation score is unreliable ("insufficient data").
+# Calculates a conservation score with confidence interval for each amino acid. Classifies the conservation scores into nine levels, and maps them to standard conservation level colors (see color key at the top of this page). Marks residues for which the conservation score confidence interval is too large, hence the conservation score is unreliable ("insufficient data").
 # Displays the protein, colored by conservation, in interactive 3D, using [[FirstGlance in Jmol]], [[Chimera]], [[PyMOL]], or [[Protein Explorer]].
-Unlike ConSurf-DB, the ConSurf Server does '''no filtering''' of the gathered sequences before constructing the MSA (except to eliminate 99% redundant sequences). If the number of sequences obtained is too small, it is up to the user to run another job with parameters adjusted to obtain more sequences. Because sequences with &lt;99% redundancy are not filtered out, it usually takes more than the default 50 sequences to obtain an optimally informative result.
 ==Examples==