PROBALIGN(1)

💖 PROBALIGN 💖

okay bestie, gather round, because this is the one that aligns your protein sequences and it's lowkey iconic 👑

🦋 NAME 🦋

probalign — align sequences in MFAFILE(s) and print the result to standard output. that's it, that's the whole vibe. no cap.

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✨ DESCRIPTION ✨

so PROBALIGN Version 1.4 (Nov 2010) takes a whole bunch of multiple protein sequences, aligns them, and prints the result straight to standard output. main character energy fr fr. it was written by Satish Chikkagoudar and Usman Roshan, using code from PROBCONS version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein). a whole collab. the girls are working together 💅

PROBALIGN 1.4 comes with ABSOLUTELY NO WARRANTY. like, none. zero. it's free software though, and you're welcome to redistribute it under certain conditions — check the README file for the deets, bestie 📄

🎀 Usage:

probalign [OPTION]... [MFAFILE]...

🌸 Description:

Align sequences in MFAFILE(s) and print result to standard output. that's the assignment and it ate ✨

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👑 OPTIONS 👑

here's where it gets juicy. every flag, one by one, no skipping:

• -clustalw — use CLUSTALW output format instead of MFA. switching up the lewk 💅
• -v, --verbose — report progress while aligning (default: off). turn this on if you're the type who needs to see the bar move, iykyk
• -a, --alignment-order — print sequences in alignment order rather than input order (default: off). so it reorders the girlies based on how they aligned, not how you fed them in 🫶
• -T, -temperature — sets the thermodynamic temperature parameter. default: 5 (for protein data mode), 1 (for nucleotide data mode). it's giving thermodynamics, it's giving science 🌡️
• -score_matrix, --score_matrix — sets the type of scoring matrix used to calculate the posterior probabilities (default: gonnet_160, representing gonnet 160 — refer to the README for details). the README is your bestie here, go read it 📖
• -go, --gap-open — this option can be used to specify the gap open parameter. the default for Gonnet 160 (protein) is 22 and for nucleotide (simple matrix) it's 4. gaps gotta open somewhere, periodt ✂️
• -ge, --gap-extension — this option can be used to specify the gap extension parameter. the default for Gonnet 160 (protein) is 1 and for nucleotide (simple matrix) it's 0.25. and once a gap is open, it extends, no cap 📏
• -nuc — specify this option to indicate that the inputted sequences are nucleotide sequences 🧬
• -prot — specify this option to indicate that the inputted sequences are protein sequences [DEFAULT]. so if you say nothing, this is what you get, the default queen 👑
• -showPP — outputs the posterior probabilities of alignment columns as a new sequence named Posterior Probabilities (the probability values are scaled to be between integers between 0 and 9). yes it literally names a sequence that, it's so extra and I'm obsessed 💀✨

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🌈 reminder: no warranty, free software, redistribute responsibly, and go read the README. that's the whole rules of the house 🏠

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and that's the page, bestie 🎀 this was probalign 1.4, brought to you from January 2023 — align responsibly, mwah 💖🌸🦋