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 nonsynonymous polymorphisms and laboratory-induced missense mutations.
How to Use
SIFT uses environment modules. Typemodule load SIFT
SIFT scores for mutations can be run using a FASTA file aligned to a reference database.seqs_chosen_via_median_info.csh $SIFTHOME/test/lacI.fasta /fdb/blastdb/nr 2.75 cp $SIFT_SCRATCHDIR/lacI.alignedfasta .
SIFT can also generate scores for variants. The databases for SIFT are located in $SIFTDB.SIFT_exome_nssnvs.pl -i $SIFTHOME/test/snvs_build37.input \ -d $SIFTDB/Human_db_37 -o $SIFT_SCRATCHDIR -z output.tsv
Here is an example SIFT script to run on the cluster:# this file is sift_script.sh clearscratch module load SIFT SIFT_exome_nssnvs.pl -i $SIFTHOME/test/snvs_build37.input \ -d $SIFTDB/Human_db_37 -o $SIFT_SCRATCHDIR -z output.tsv
Then, submit to a g24 node, since these nodes have at least 120GB of disk space on /scratch:qsub -l nodes=1:c16:g24 sift_script.sh