NAME

       SIFT_for_submitting_fasta_seq.csh - predict effect of an amino acid substitution on
       protein function

SYNOPSIS

       SIFT_for_submitting_fasta_seq.csh <FASTA_FILE> <BLAST_DB> <SUBSTITUTIONS_FILE>
       [BLAST_PROCESSORS]

DESCRIPTION

       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.

OPTIONS

       <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.

EXAMPLES

        SIFT_for_submitting_fasta_seq.csh /usr/share/doc/sift/examples/lacI.fasta [BLAST_DB] /usr/share/doc/sift/examples/lacI.subst

AUTHOR

       Pauline Ng

COPYRIGHT AND LICENSE

       (C) Copyright 1993-2001, Fred Hutchinson Cancer Research Center

       Noncommercial license. See /usr/share/doc/sift/copyright for details.

SEE ALSO

       info_on_seqs