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seq.fas : amino acid sequence of the selected chain in fasta format.
seq.blast.zip : psi-blast output (zippped) for the sequence. The database which was used can be found at the beginning of the file, in the line begins with: 'Database'.
seq_homologs.fasta : file containing the sequences selected by the screening process, in fasta format.
cd-hit.out.clstr : output of the program cd-hit, which is showing the clusters that was found from all the selected sequences.
seq_rejected.txt : file containing the sequences rejected by the screening process and the reason for their rejection.
seq_final.fasta : The final file which details the screened sequences in fasta format.
TheTree.txt : Tree in newick format, which was constructed in the neighbor joining method from the chosen sequences.
msa.aln : Multiples Sequence Alignment, created using MUSCLE.
msa_aa_variety_percentage.csv : table which details the amino acid variety in each position in the MSA (best viewed with an editor that respects Comma-Separated Values).
r4sOrig.res : Rate4Site output, before the normalization.
r4s.res : Rate4Site output, after the normalization.
consurf.grades : this file gives the most information which sums up ConSurf run: Assigns each position in the MSA and each residue in the PDB with a conservation grade, shows the normalizes score from rate4site, residue variety for each position and more.
rasmol.scr : a rasmol script which colors each ATOM in the PDB with the relevant conservation grade. This script does not show insufficient data: the estimated score will be assigned with the residue.
isd_rasmol.scr : same as rasmol.scr, only in this script the insufficient data will be shown as light yellow color.
(pdbid_chain)_ConSurf_DB_pipe.pdb : Header which should be added to the beginning of the PDB file in order to view the PDB molecule with FirstGlance in JMOL. (Please note that the line beginning with the word 'HEADER' should be removed from the PDB file).