Phylogeny-based Protein Function Prediction

SIFTER (Statistical Inference of Function Through Evolutionary Relationships) is a statistical approach to predicting protein function that uses a protein family's phylogenetic tree, as the natural structure for representing protein relationships.

Predict by Protein ID

Find SIFTER predictions for your query proteins.

Enter query proteins

Paste the Uniprot IDs or Accession numbers of your query proteins
separate IDs by a space, comma, semicolon, or enter one ID per line

Predict for all proteins of a Species

Find SIFTER predictions for proteins in your query species.

Find proteins that have given Functions

For a set of query functions, find proteins with high probability of having those functions.

  • This option searches across the given species to identify proteins that are predicted by SIFTER to have any of the query functions as their top predictions.

Predict for homologs of given Sequences

Find SIFTER predictions fo the closest homologs of the query sequences.

  • We BLAST search across 16,853,547 proteins (wihich already has SIFTER predictions) to identify close homologs to the query sequences.

Enter query sequences

Paste (up to 10) protein sequences in FASTA format
Show advanced options


  • SIFTER was recently honored as the best-performing sequence-based protein function prediction method in the Critical Assessment of Function Annotation.
  • SIFTER webserver is updated on Aug 12,2015:
    • Results are obtained using the family data from Pfam v27.0, the gene ontology data from GO (update 03/31/2015), and the annotation data from UniProt-GOA (update 03/31/2015).
    • Currently SIFTER has predictions for proteins across species.
  • For queries not in our current results, try "Predict by seqence" to find SIFTER predictions for the closest homologs.
  • Citations:
    • Sahraeian SME, Luo KR, Brenner SE. 2015. SIFTER search: a web server for accurate phylogeny-based protein function prediction. Nucleic Acids Research. Nucleic Acids Research 43:W141-W147. doi:10.1093/nar/gkv461
    • Engelhardt BE, Jordan MI, Srouji JR, Brenner SE. 2011. Genome-scale phylogenetic function annotation of large and diverse protein families.Genome Research 21:1969-1980. doi:10.1101/gr.104687.109