ConSurfDB vs. ConSurf: Difference between revisions

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

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 In brief, the  [http://consurf.tau.ac.il ConSurf Server] uses the following process by default:
 # Obtains the protein sequence for the specified PDB code (or uploaded PDB file) and chain.
-# Gathers closely related sequences from Swiss-Prot (or Uniprot) with a PSI-BLAST search. E value cutoff<ref name="evalue" />, number of iterations, and number of sequences to use are configurable.
+# Gathers closely related sequences from Swiss-Prot (or a larger database that you specify) with a PSI-BLAST search. E value cutoff<ref name="evalue" />, number of iterations, and number of sequences to use are configurable.
-# Eliminates non-unique sequences, namely, those that are 99% or more identical with another sequence.
+# 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.)
 # Constructs a phylogenetic tree. (Or you can upload your own.)