Upload your Multiple Sequece Alignment file:
ConSurf accepts external MSAs in the 7 formats supported by CLUSTAL W
. These are: NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF and RSF format.
In case you provide an external MSA file in Fasta format, please use the "-" sign as the only gap symbol, as this is the only standard gap sign that ConSurf accepts.
Indicate the Query Sequence Name:
This should be the exact name of the sequence in the provided MSA file, that corresponds to the query protein.
Upload your TREE file (in Newick format):
In case you provide an external multiple sequence alignment (MSA) file, ConSurf can also accept a corresponding external phylogenetic tree in Newick (Phylip) format, for example: Tree File
The names of the proteins sequences in the tree file must be identical to the names in the MSA file.
- a curated protein sequence database which strives to provide a high level of annotation
Clean UniProt - a modified version of the UniProt database aimed to screen the more reliable sequences.UniRef90
- database cluster sequences and sub-fragments with 11 or more residues that have at least 90% sequence identity with each other (from any organism) into a single UniRef entry, displaying the sequence of a representativeUniProt
is the universal protein resource, a central repository of protein data created by combining Swiss-Prot, TrEMBL and PIR.
Maximum Homolougs to collect
Maximal %ID Between Sequences
Minimal %ID For Homologs
PSI-BLAST E-value Cutoff
Homolog search algorithm
Let me select the sequences for the analysis manually out of Blast results
The calculation method for the rate of evolution at each site in the MSA.
The Bayesian method was shown to significantly improve the accuracy of conservation scores estimations over the Maximum Likelihood method, in particular when a small number of sequences are used for the calculations. An additional advantage of the Bayesian method is that a confidence interval is assigned to each of the inferred evolutionary conservation score.
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