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SIFT:Submit aligned sequences

# SIFT: Submit aligned sequences

Submit your query sequence along with other protein sequences that are aligned to it for SIFT. Your query sequence is the sequence that you would like prediction on (i.e. the sequence in which you have introduced the amino acid substitutions). The query sequence should be first in the alignment. The positions of amino acid substitutions should be with respect to the query sequence. Partial sequences should be flanked by Xes at the beginning and end of the sequence so that those positions are not considered gaps (and hence have liberal prediction).
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Enter alignment
Enter your protein query sequence aligned with related protein sequences. These protein sequences are assumed to be functional, and is what SIFT will base its prediction on. The normal (functional) query sequence should appear first.
Enter the name of the file containing your aligned protein sequences [clustal, msf, or fasta format].
-or-
Paste in your aligned protein sequences [clustal, msf, or fasta format].

Substitutions to be predicted on (can be left blank)
Enter the name of file containing substitutions of interest: [format]:
-or-
Enter the substitutions of interest: [format]:

Parameters
Remove sequences more than percent identical to query
This cleans out any polymorphic alleles (sequences in the alignment that are nearly identical to your protein but already containing the substitutions of interest). The contaminating sequences may cause the substitution to be predicted as tolerated.