1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
|
=head1 NAME
SIFT_for_submitting_fasta_seq.csh - predict effect of an amino acid substitution on protein function
=head1 SYNOPSIS
SIFT_for_submitting_fasta_seq.csh <FASTA_FILE> <BLAST_DB> <SUBSTITUTIONS_FILE> [BLAST_PROCESSORS]
=head1 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 F<< ./<seq_file>.SIFTprediction >>.
This program is used for FASTA input and is part of the SIFT suite.
=head1 OPTIONS
=over
=item <FASTA_FILE>
Protein sequence in fasta format.
=item <BLAST_DB>
Protein database to search. These sequences are assumed to be functional.
=item <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.
=item [BLAST_PROCESSORS]
Number of processors/cores to use when running blast via the B<-a> argument.
=back
=head1 EXAMPLES
SIFT_for_submitting_fasta_seq.csh /usr/share/doc/sift/examples/lacI.fasta [BLAST_DB] /usr/share/doc/sift/examples/lacI.subst
=head1 AUTHOR
Pauline Ng
=head1 COPYRIGHT AND LICENSE
(C) Copyright 1993-2001, Fred Hutchinson Cancer Research Center
Noncommercial license. See /usr/share/doc/sift/copyright for details.
=head1 SEE ALSO
L<info_on_seqs>
|
