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SIFT_for_submitting_fasta_seq.csh - predict effect of an amino acid substitution

SIFT_FOR_SUBMITTING_FASTA_SEQ.CSH(1) User Commands SIFT_FOR_SUBMITTING_FASTA_SEQ.CSH(1)

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 (C) Copyright 1993-2001, Fred Hutchinson Cancer Research Center
Noncommercial license. See /usr/share/doc/sift/copyright for details.

SEE ALSO

info_on_seqs
2012-10-08 4.0.3b