PolyPhenDbColumns | R Documentation |
Description of the PolyPhen Sqlite Database Columns
These column names are displayed when columns
is called on a
PolyPhenDb
object.
rsid : rsid
Original query :
OSNPID : original SNP identifier from user input
OSNPACC : original protein identifier from user input
OPOS : original substitution position in the protein sequence from user input
OAA1 : original wild type (reference) aa residue from user input
OAA2 : original mutant (reference) aa residue from user input
Mapped query :
SNPID : SNP identifier mapped to dbSNP rsID if available, otherwise same as o_snp_id. This value was used as the rsid column
ACC : protein UniProtKB accession if known protein, otherwise same as o_acc
POS : substitution position mapped to UniProtKB protein sequence if known, otherwise same as o_pos
AA1 : wild type aa residue
AA2 : mutant aa residue
NT1 : wild type allele nucleotide
NT2 : mutant allele nucleotide
PolyPhen-2 prediction :
PREDICTION : qualitative ternary classification FPR thresholds
PolyPhen-1 prediction :
BASEDON : prediction basis
EFFECT : predicted substitution effect on the protein structure or function
PolyPhen-2 classifiers :
PPH2CLASS : binary classifier outcome ("damaging" or "neutral")
PPH2PROB : probability of the variation being dammaging
PPH2FPR : false positive rate at the pph2_prob level
PPH2TPR : true positive rate at the pph2_prob level
PPH2FDR : false discovery rate at the pph2_prob level
UniProtKB-SwissProt derived protein sequence annotations :
SITE : substitution SITE annotation
REGION : substitution REGION annotation
PHAT : PHAT matrix element for substitution in the TRANSMEM region
Multiple sequence alignment scores :
DSCORE : difference of PSIC scores for two aa variants (Score1 - Score2)
SCORE1 : PSIC score for wild type aa residue (aa1)
SCORE2 : PSIC score for mutant aa residue (aa2)
NOBS : number of residues observed at the substitution position in the multiple alignment (sans gaps)
Protein 3D structure features :
NSTRUCT : initial number of BLAST hits to similar proteins with 3D structures in PDB
NFILT : number of 3D BLAST hits after identity threshold filtering
PDBID : protein structure identifier from PDB
PDBPOS : position of substitution in PDB protein sequence
PDBCH : PDB polypeptide chain identifier
IDENT : sequence identity between query and aligned PDB sequences
LENGTH : PDB sequence alignment length
NORMACC : normalized accessible surface
SECSTR : DSSP secondary structure assignment
MAPREG : region of the phi-psi (Ramachandran) map derived from the residue dihedral angles
DVOL : change in residue side chain volume
DPROP : change in solvent accessible surface propensity resulting from the substitution
BFACT : normalized B-factor (temperature factor) for the residue
HBONDS : number of hydrogen sidechain-sidechain and sidechain-mainchain bonds formed by the residue
AVENHET : average number of contacts with heteroatoms per residue
MINDHET : closest contact with heteroatom
AVENINT : average number of contacts with other chains per residue
MINDINT : closest contact with other chain
AVENSIT : average number of contacts with critical sites per residue
MINDSIT : closest contact with a critical site
Nucleotide sequence features (CpG/codon/exon junction) :
TRANSV : whether substitution is a transversion
CODPOS : position of the substitution within the codon
CPG : whether or not the substitution changes CpG context
MINDJNC : substitution distance from exon/intron junction
Pfam protein family :
PFAMHIT : Pfam identifier of the query protein
Substitution scores :
IDPMAX : maximum congruency of the mutant aa residue to all sequences in multiple alignment
IDPSNP : maximum congruency of the mutant aa residue to the sequence in alignment with the mutant residue
IDQMIN : query sequence identity with the closest homologue deviating from the wild type aa residue
Comments :
COMMENTS : Optional user comments
Valerie Obenchain
?PolyPhenDb
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