MAFFT-HOMOLOGS(1)

✨ NAME ✨

mafft-homologs — the little script that aligns your sequences together with their homologues, and it goes and collects those homologues from SwissProt all by itself via NCBI BLAST. bestie it's giving personal assistant energy fr fr 💅

(this is the manual page for MAFFT-HOMOLOGS(1), in case you were wondering where you wandered into 🎀)

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🌸 SYNOPSIS 🌸

mafft-homologs [options] input [> output]

like… you give it input, you get alignment. pipe it out with > output if that's your vibe. ✨

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🦋 DESCRIPTION 🦋

okay so here's the tea ☕ — when you've got a few sequences that are only distantly related, their alignment gets way better if you align them together with their close homologs. like, considerably improved. slay.

and why is that, you ask? probably the same reason PSI-BLAST works, no cap. the close homologs bring extra info to the table: the positions of highly conserved residues, the spots with lots of gaps, and other little clues. basically they're the friends who show up and suddenly the group photo looks good 📸

according to Katoh et al. (2005), the improvement from adding close homologs is 10% or so — which is comparable to the improvement you'd get by incorporating structural information of a pair of sequences. iconic honestly.

and here's how mafft-homologs rolls on a mafft server:

1. Collect a number (50 by default) of close homologs (E=1e-10 by default) of the input sequences. 🫶
2. Align the input sequences and homologs all together using the L-INS-i strategy.
3. Remove the homologs. (they did their job, they can go home now 💀)

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💖 OPTIONS 💖

• -a n — how many sequences to collect. default: 50. 🎀
• -e n — the threshold value. default: 1e-10. 👑
• -o xxx — options that get handed to mafft. default: " --op 1.53 --ep 0.123 --maxiterate 1000 --localpair --reorder". yes that's the whole string, spaces and all, don't come for me.
• -l — does the BLAST searches locally instead of using NCBI BLAST. heads up: this requires locally installed BLAST and a database, so it's not a "just vibe and it works" situation. 😭
• -f — also outputs the collected homologues. default: off. 🙈
• -w — subjects the entire sequences to the BLAST search. default: only the well-aligned region. 🌈

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🌟 REQUIREMENTS 🌟

• MAFFT version > 5.58. (like, strictly greater. don't try it on 5.58 itself, bestie. 💀)

and then you need either of these:

• lynx — for when the remote BLAST server is being used. 🧚
• BLAST and a protein sequence database — for when local BLAST is being used. 🍓

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📚 REFERENCES 📚

Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment.

(cite your sources, it's the law of academia 💜)

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👀 SEE ALSO 👀

• mafft(1)

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💜 AUTHORS 💜

• Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.> — wrote Mafft. the legend themselves. 🔥
• Charles Plessy <charles-debian-nospam@plessy.org> — wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template. 🫶

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⭐ COPYRIGHT ⭐

• Copyright © 2002-2007 Kazutaka Katoh (mafft)
• Copyright © 2007 Charles Plessy (this manpage)

Mafft and its manpage are offered under the following conditions:

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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okay that's the whole page bestie, go align something gorgeous 🦋

this has been mafft-homologs 2.1, dated 2007-06-09 — old but gold, lowkey iconic, periodt 💅✨