http://mutationassessor.org/r3/?cm=var&p=<protein ID>&var=<variant>

http://mutationassessor.org/r3/?cm=var&var=<genomic substitution>

for example :

http://mutationassessor.org/r3/?cm=var&p=EGFR_HUMAN&var=G719S

http://mutationassessor.org/r3/?cm=var&var=7,55211080,G,A

http://mutationassessor.org/r3/?cm=var&var=hg38,13,32338418,G,T

 

To get tab-separated text add frm=txt, to get all available fields add fts=all

for example :

http://mutationassessor.org/r3/?cm=var&var=7,55211080,G,A&fts=all&frm=txt

 

To get a JSON format array of objects add frm=json

To select fields for each JSON object add a comma separated list of Specifiers (see page bottom) fts=colspec1,...,colspecN

for example :

http://mutationassessor.org/r3/?cm=var&var=7,55211080,G,A&frm=json&fts=input,gene,msa,pdb,F_impact,F_score,rsport,msa_height

http://mutationassessor.org/r3/?cm=msa&ty=f&p=<protein ID>&rb=<domain start>&re=<domain end>&var=<variant>

for example :

http://mutationassessor.org/r3/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G719S

http://mutationassessor.org/r3/pdb.php?prot=<protein ID>&from=<domain start>&to=<domain end>&var=<variant>

for example :

http://mutationassessor.org/r3/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G719S

 

to specify a particular PDB structure and chain add pc=<PDB code>:<PDB chain>

for example :

http://mutationassessor.org/r3/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G719S&pc=1m14:A

Domain boundaries provided to other API functions must correspond to a MSA built and stored in the database.

To get a list of all MSA built for a particular protein use this command:

http://mutationassessor.org/r3/?cm=domains&p=<protein ID>

for example :

http://mutationassessor.org/r3/?cm=domains&p=EGFR_HUMAN

 

to get it as a tab-separated table for automatic parsing, or JSON format arry of objects; add frm=txt, or frm=json

for example :

http://mutationassessor.org/r3/?cm=domains&p=EGFR_HUMAN&frm=txt

http://mutationassessor.org/r3/?cm=domains&p=EGFR_HUMAN&frm=json

To get the specificity scores and conservation scores per alignment column for all MSA built for a particular protein use this command:

http://mutationassessor.org/r3/?cm=residues&p=<protein ID>

for example :

http://mutationassessor.org/r3/?cm=residues&p=EGFR_HUMAN

 

to get it as a tab-separated table for automatic parsing add frm=txt

for example :

http://mutationassessor.org/r3/?cm=residues&p=EGFR_HUMAN&frm=txt

 

To get a JSON format array of objects add frm=json

To only show residues positions which are within the used range for variant score access add igf=yes

for example :

http://mutationassessor.org/r3/?cm=residues&p=EGFR_HUMAN&frm=json&igf=yes

 

Notes on output:

- output will only be generated for MSA which have been previously built.

- some constructed alignments overlap others, and then part of an alignment may be unused for score lookup.

- field align# shows the alignment number (for example, with 2 alignments, this will be '1' or '2')

- field inner_flag is ('1', or '0') if this column of the alignment (is, or is not) used for score lookup.

- field residue# is the residue position in the uniprot protein sequence.

- field residue is the amino acid residue code in the uniprot protein sequence.

- field cons_score is the entropy based score for conservation in the column. Lower scores mean greater conservation.

- field cons_flag is ('1', or '0') if this column (is, or is not) flagged as a low conservation scoring column.

- field spec_score is the entropy based score for specificity in the column. Higher scores mean greater specificity.

- field spec_flag is ('1', or '0') if this column (is, or is not) flagged as a high specificity scoring column.

- columns are flagged if they are in the most significant 17% of the total score range for the relevant score type.

http://mutationassessor.org/r3/chr.php?pos=<genome build>,<chromosome>,<position>

To get a JSON format array of objects add frm=json

for example :

http://mutationassessor.org/r3/chr.php?pos=hg19,9,98209229

http://mutationassessor.org/r3/chr.php?pos=hg19,9,98209229&frm=json

Column name	Specifier	Description
Mutation	input	Mutations as given by the user
RG variant	rgaa	Variant based on reference genome (for submitted in genomic coordinates)
RG variant type	rgvt	Variant type based on reference genome: missense,silent,stop loss,nonsense (for submitted in genomic coordinates)
User data	data	Optional user data
MSA	msa	Link to multiple sequence alignment browser
PDB	pdb	Link to 3D structure browser
Func.Impact	F_impact`	Functional impact of a variant : predicted functional (high, medium), predicted non-functional (low, neutral). Please see paper for details.
FI score	F_score	Functional impact combined score
VC score	vc_score	Variant conservation score
VS score	vs_score	Variant specificity score
Mapping issue	info	Issue with variant/protein mapping
AA variant	var	Amino-acid substitution
Gene	gene	Gene name
Uniprot	uprot	Uniprot protein accession ID
Refseq	rsprot	Refseq protein ID
gaps in MSA	gaps	Portion of gaps in variant position in multiple sequence alignment
MSA height	msa_height	Number of diverse sequences in multiple sequence alignment (identical or highly similar sequences filtered out)
Codon start position	chr	Start of a codon
Uniprot position	up_pos	Variant position in Uniprot protein, can be different from the one in Refseq
Uniprot residue	up_res	Reference residue in Uniprot protein, can be different from the one in Refseq
Refseq position	rs_pos	Variant position in Refseq protein, can be different from the one in Uniprot
Refseq residue	rs_res	Reference residue in Refseq protein, can be different from the one in Uniprot
N.Cosmic	cnt_cosmic	Number of mutations in COSMIC for this protein
N.SNPs	cnt_snps	Number of SNPs in dbSNP for this protein
Protein b.site	bs_prot	Variant position maps to PDB residue which is in a binding site with another protein
DNA/RNA b.site	bs_dna	Variant position maps to PDB residue which is in a binding site with DNA/RNA molecule
small.mol b.site	bs_smol	Variant position maps to a PDB residue that is in a binding site with a small molecule. Only the first 4 are shown in the main table - browse through mapped PDB structures to see all small molecules. The following small molecules are ignored: PO4,PI,SO4,SUL,CL,BR,NO3,SCN,NH4,K,NA,LI,MG,DOD,NAG,MAN,GOL,SO4,CL,CO3,FS4 (source:Polyphen)