SIFT_for_submitting_fasta_seq.csh - predict effect of an amino acid substitution
on protein function
SIFT_for_submitting_fasta_seq.csh <FASTA_FILE> <BLAST_DB>
<SUBSTITUTIONS_FILE> [BLAST_PROCESSORS]
SIFT predicts whether an amino acid substitution affects protein function based
on sequence homology and the physical properties of amino acids.
Results are stored in
./<seq_file>.SIFTprediction.
This program is used for FASTA input and is part of the SIFT suite.
- <FASTA_FILE>
- Protein sequence in fasta format.
- <BLAST_DB>
- Protein database to search. These sequences are assumed to
be functional.
- <SUBSTITUTIONS_FILE>
- File of substitutions to be predicted. See
/usr/share/doc/sift/examples/lacI.subst for an example of the format. If
you give '-', scores for all mutations of the entire protein sequence are
printed.
- [BLAST_PROCESSORS]
- Number of processors/cores to use when running blast via
the -a argument.
SIFT_for_submitting_fasta_seq.csh /usr/share/doc/sift/examples/lacI.fasta [BLAST_DB] /usr/share/doc/sift/examples/lacI.subst
Pauline Ng
(C) Copyright 1993-2001, Fred Hutchinson Cancer Research Center
Noncommercial license. See /usr/share/doc/sift/copyright for details.
info_on_seqs