predictions of functional sites sift_variants_wrapper.sh "$input" "$output" "${input.metadata.dbkey}" "${GALAXY_DATA_INDEX_DIR}/sift_db.loc" "$chrom_col" "$pos_col" "$base" "$allele_col" "$strand_source.strand_col" "$output_opts" zero-based one-based a column in the dataset all on sense/forward/+ strand all on antisense/reverse/- strand Ensembl Gene ID Gene Name Gene Description Ensembl Protein Family ID Ensembl Protein Family Description Ensembl Transcript Status (Known / Novel) Protein Family Size Ka/Ks (Human-mouse) Ka/Ks (Human-macaque) OMIM Disease Allele Frequencies (All Hapmap Populations - weighted average) Allele Frequencies (CEU Hapmap population) awk rm sed

.. class:: warningmark This currently works only for builds hg18 or hg19. ----- **Dataset formats** The input and output datasets are tabular_. (`Dataset missing?`_) .. _tabular: ./static/formatHelp.html#tab .. _Dataset missing?: ./static/formatHelp.html ----- **What it does** SIFT predicts whether an amino-acid substitution affects protein function, based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring non-synonymous polymorphisms and laboratory-induced missense mutations. This tool uses SQLite databases containing pre-computed SIFT scores and annotations for all possible nucleotide substitutions at each position in the human exome. Allele frequency data are from the HapMap frequency database, and additional transcript and gene-level data are from Ensembl BioMart. The input dataset must contain columns for the chromosome, position, and alleles. The alleles must be two nucleotides separated by '/', usually the reference allele and the allele of interest. The strand must either be in another column or all the same. The output contains a standard set of columns plus the additional ones that have been selected from the list above. Website: http://sift.jcvi.org/ ----- **Example** - input file:: chr3 81780820 + T/C chr2 230341630 + G/A chr2 43881517 + A/T chr2 43857514 + T/C chr6 88375602 + G/A chr22 29307353 - T/A chr10 115912482 - G/T chr10 115900918 - C/T chr16 69875502 + G/T etc. - output file:: #Chrom Position Strand Allele Codons Transcript ID Protein ID Substitution Region dbSNP ID SNP Type Prediction Score Median Info Num seqs at position User Comment chr3 81780820 + T/C AGA-gGA ENST00000264326 ENSP00000264326 R190G EXON CDS rs2229519:C Nonsynonymous DAMAGING 0.04 3.06 149 chr2 230341630 + G/T - ENST00000389045 ENSP00000373697 NA EXON CDS rs1803846:A Unknown Not scored NA NA NA chr2 43881517 + A/T ATA-tTA ENST00000260605 ENSP00000260605 I230L EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7 chr2 43857514 + T/C TTT-TcT ENST00000260605 ENSP00000260605 F33S EXON CDS rs2288709:C Nonsynonymous TOLERATED 0.61 3.33 6 chr6 88375602 + G/A GTT-aTT ENST00000257789 ENSP00000257789 V217I EXON CDS rs2307389:A Nonsynonymous TOLERATED 0.75 3.17 13 chr22 29307353 + T/A ACC-tCC ENST00000335214 ENSP00000334612 T264S EXON CDS rs42942:A Nonsynonymous TOLERATED 0.4 3.14 23 chr10 115912482 + C/A CGA-CtA ENST00000369285 ENSP00000358291 R179L EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2 chr10 115900918 + G/A CAA-tAA ENST00000369287 ENSP00000358293 Q271* EXON CDS rs7095762:T Nonsynonymous N/A N/A N/A N/A chr16 69875502 + G/T ACA-AaA ENST00000338099 ENSP00000337512 T608K EXON CDS rs3096381:T Nonsynonymous TOLERATED 0.12 3.41 3 etc. ----- **References** Ng PC, Henikoff S. (2001) Predicting deleterious amino acid substitutions. Genome Res. 11(5):863-74. Ng PC, Henikoff S. (2002) Accounting for human polymorphisms predicted to affect protein function. Genome Res. 12(3):436-46. Ng PC, Henikoff S. (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 31(13):3812-4. Kumar P, Henikoff S, Ng PC. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 4(7):1073-81. Epub 2009 Jun 25.