ALIEN_HUNTER(1)

✨ ALIEN_HUNTER(1) — User Commands 🦋

Hiii bestie, okay so this is the manual page for alien_hunter 👽💖 It's a User Commands page, and honestly the whole thing is giving main character energy.

🌸 NAME 🌸

okay so alien_hunter is the Interpolated Variable Order Motifs tool for spotting horizontally acquired DNA 🧬✨ basically, it hunts down DNA that snuck in from somewhere else 🕵️‍♀️

💅 SYNOPSIS 💅

alien_hunter <sequence.file> <output.file> [Options]

🎀 DESCRIPTION 🎀

Alien_hunter is an app that predicts putative Horizontal Gene Transfer (HGT) events using Interpolated Variable Order Motifs (IVOMs) 🔥 The IVOM approach looks at compositional biases with variable order motif distributions, and it captures the local composition of a sequence way more reliably than fixed-order methods, no cap 💯

You can optionally parse the predictions into a 2-state 2nd order Hidden Markov Model (HMM), inside a change-point detection framework 🧠 This tightens up where the boundaries of the predicted regions land, which is lowkey iconic 🙌

The predictions (in embl format) can be auto-loaded into the Artemis genome viewer, which is freely available at: http://www.sanger.ac.uk/Software/Artemis/ 🌈

INPUT: raw genomic sequence PREDICTION: HGT regions based on Interpolated Variable Order Motifs (IVOMs)

🧚 Arguments 🧚

<sequence.file>

The raw genomic sequence you feed in 🧬

<output.file>

The filename where all your output data gets saved 💾

🍓 Optional arguments 🍓

• -a — loads the prediction file straight into Artemis 💜
• -c — optimizes the predicted boundaries with a change-point detection 2 state 2nd order HMM ✨

🦋 Output files 🦋

• <output.file> — predictions (tab file) in embl format 🌸
• <output.file>.opt — optimized (HMM) predictions (tab file) in embl format 🫶
• <output.file>.plot — predictions in Artemis User Plot format, which you load manually using Graph -> Add User Plot... 📈
• <output.file>.opt.plot — optimized (HMM) predictions in Artemis User Plot format, also loaded manually using Graph -> Add User Plot... 📊
• <output.file>.sco — the scores over all the sliding windows, handy for checking the score distribution 👀

Note: predictions that overlap with an rRNA operon get mentioned in the note qualifier 🙈

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👑 SEE ALSO 👑

The manuscript describing the alien_hunter algorithm is in Bioinformatics: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Vernikos GS, Parkhill J Bioinformatics. 2006;. PMID: 16837528 📚💕

🫶 AUTHOR 🫶

This manual page was written by Andreas Tille <tille@debian.com> for the Debian(TM) system (but others are welcome to use it) 🌈 It's released under the same conditions as the software, which is GPL 💜

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alien_hunter 1.7 · October 2009 · ALIEN_HUNTER(1) — signing off, bestie, stay curious and keep those aliens caught 👽🦋💖