- Obtain amino acid sequence of 3D chain in PDB file specified by user.
- Run PSI-BLAST to find the most similar sequences in
By default uses up to 50 sequences with
E < 0.001.
- Align sequences with
Optionally, user may supply the sequence alignment.
- Construct phylogenetic tree from sequence alignment.
Optionally, user may supply the tree.
- Calculate conservation grades (and confidence intervals)
for each residue in the 3D chain
- Color the 3D model by conservation grades
in FirstGlance in Jmol or Protein Explorer.