SIFT_FOR_SUB...FASTA_SEQ.CSH(1)

✨ SIFT_for_submitting_fasta_seq.csh — the girlies' guide to predicting protein drama ✨

okay so bestie, you know SIFT_for_submitting_fasta_seq.csh? it's a User Commands page from the SIFT suite 6.2.1, dated 2026-10-09, and it's literally the FASTA-input girlie of the family. she predicts whether an amino acid substitution messes with protein function. no cap. 💅

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🌸 NAME 🌸

SIFT_for_submitting_fasta_seq.csh — predict the effect of an amino acid substitution on protein function. she's giving molecular fortune teller energy and honestly? iconic. 🧚

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🦋 SYNOPSIS 🦋

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

four lil slots, three of them mandatory, the last one optional because she's flexible like that. 💖

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💜 DESCRIPTION 💜

so what does she actually do? SIFT predicts whether an amino acid substitution affects protein function, and she does it based on sequence homology plus the physical properties of amino acids. like, she's cross-referencing your protein's whole friend group to figure out if one lil swap is gonna cause problems. 🫶

results get stored in ./<seq_file>.SIFTprediction — right there in your current directory, no hiding, no games. main character output file behavior honestly. 😭

this program is the one you reach for when your input is FASTA, and yes she is part of the SIFT suite. periodt. ✨

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🎀 OPTIONS 🎀

• <FASTA_FILE> — your protein sequence, in fasta format. this is the queen herself, the star of the show. 👑
• <BLAST_DB> — the protein database to search. important tea: these sequences are assumed to be functional. so like, she trusts you on that one. don't betray her. 🥺
• <SUBSTITUTIONS_FILE> — the file of substitutions you want predicted. peep /usr/share/doc/sift/examples/lacI.subst for an example of the format, because format guesses are not the vibe. and here's the cute lil party trick: if you pass '-' (just a dash, bestie), then scores for all mutations of the entire protein sequence get printed. the whole glow-up, every single one. 🍓
• [BLAST_PROCESSORS] — number of processors/cores to use when running blast via the -a argument. optional! sprinkle it in when you're feeling impatient and want her to move faster. 🔥

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🌈 EXAMPLES 🌈

here's the whole thing in action, exactly as written, because we do not paraphrase commands in this house:

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

see how [BLAST_DB] is sitting there in brackets? that's your placeholder to fill in with your actual database. don't literally type the brackets, i'm begging. 💀

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👑 AUTHOR 👑

Pauline Ng. the blueprint. the original. we stan. 💖

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⭐ COPYRIGHT AND LICENSE ⭐

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

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

heads up bestie: this one is noncommercial — read /usr/share/doc/sift/copyright before you go using it for anything with a price tag on it. no exceptions, she's serious. 🙈

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💫 SEE ALSO 💫

• info_on_seqs

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and that's the whole page, babes — she's 6.2.1, she's dated 2026-10-09, she's a User Commands girlie, and she's out here predicting protein plot twists one substitution at a time. go fill in your FASTA and slay. 💅✨🦋