HELP

Input data are a protein sequence and amino acid variations.

Amino acid sequence

Accepted formats are the following;: ・FASTA
・Header beginning with “>” followed by 1-16 alphanumeric characters or underscore(”_”)
・No white space allowed
・Amino acids in one-letter code
・More than 30 residues

Variations

Accepted formats are the following;

<Reference amino acid><Position><Variant amino acid>　　　e.g. D15L: ・Amino acids in one-letter code
・Position indicates the location number of reference amino acid residue from the first residue in your query sequence as position 1.
・No white space allowed
・Only single site substitutions, no deletions and insertions
・A list of multiple substitutions are separated by comma(,) or linefeed.
・No more than 50 mutations

Prediction tools

	Prediction Methods	Version	Developer/Provider	Reference
PANTHER	・Evolutionary conservation	1.02	・University of Southern California (Thomas laboratory)	Website Thomas et al., 2003 Mi et al., 2012
PolyPhen2	・Evolutionary conservation ・Machine learning (Bayesian)	2.2.2r405	・Brigham & Women’s Hospital (Harvard Medical School)	Website Adzhubei et al., 2010
PROVEAN	・Evolutionary conservation	1.1	・J. Craig Venter Institute	Website Choi et al., 2012
SIFT	・Evolutionary conservation	1.03	・J. Craig Venter Institute ・A*STAR/GIS	Website1 Website2 Kumar et al., 2009

E-mail

The result URL will be sent by e-mail. Analysis may take quite some time; from several minutes to days. This service is optional, but strongly recommended.

Prediction score

The higher score represents the more neutral mutation except in PolyPhen2.

	Min. score	Cutoff	Max. score
PANTHER	-10 (Deleterious)	-3	0 (Neutral)
PolyPhen2	0 (Benign)	0.5	1 (Probably damaging)
PROVEAN	- (Deleterious)	-2.5	- (Neutral)
SIFT	0 (Deleterious)	0.05	1 (Tolerated)