Last data update: 2014.03.03

R: SIFTDb Columns
SIFTDbColumnsR Documentation

SIFTDb Columns

Description

Description of the SIFT Sqlite Database Columns

Column descriptions

These column names are displayed when columns is called on a SIFTDb object.

  • RSID : rsid

  • PROTEINID : NCBI RefSeq protein ID

  • AACHANGE : amino acid substitution; reference aa is preceeding, followed by the position and finally the snp aa

  • METHOD : method of obtaining related sequences using PSI-BLAST

  • AA : either the reference or snp residue amino acid

  • PREDICTION : SIFT prediction

  • SCORE : SIFT score (range 0 to 1)

    • TOLERATED : score is greater than 0.05

    • DAMAGING : score is less than or equal to 0.05

    • NOT SCORED : no prediction is made if there are less than 2 homologous sequences that have an amino acid at the position of the given SNP or if the SIFT prediction is not available

  • MEDIAN : diversity measurement of the sequences used for prediction (range 0 to 4.32)

  • POSITIONSEQS : number of sequences with an amino acide at the position of prediction

  • TOTALSEQS : total number of sequences in alignment

Author(s)

Valerie Obenchain

See Also

?SIFTDb

Results