PROBCONS(1)

💖 PROBCONS 💖

okay bestie, welcome to the probcons(1) glow-up page, straight outta the Probcons Manual ✨

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✨ NAME ✨

probcons — align multiple protein sequences and print to standard output 🧬💅

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🌸 SYNOPSIS 🌸

probcons [OPTION] [MFAFILE] [MFAFILE]

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🦋 DESCRIPTION 🦋

so like. probcons is THE tool for generating multiple alignments of protein sequences, no cap. it's out here combining probabilistic modeling with consistency-based alignment techniques, and because of that, PROBCONS has achieved the highest accuracies of all alignment methods to date. we're literally the main character of alignment programs 💅

and on the BAliBASE benchmark alignment database? the alignments produced by PROBCONS show statistically significant improvement over current programs. like:

• it has an average of 7% more correctly aligned columns than those of T-Coffee 😌
• 11% more correctly aligned columns than those of CLUSTAL W 🔥
• and 14% more correctly aligned columns than those of DIALIGN 👑

ate and left no crumbs fr fr.

probcons aligns sequences provided in MFA format. this format consists of multiple sequences. each sequence in MFA format begins with a single-line description, followed by lines of sequence data. and the way you tell the description line apart from the sequence data? there's a greater-than (>) symbol in the first column. iconic, honestly 🎀

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🌈 OPTIONS 🌈

• -clustalw — use CLUSTALW output format instead of MFA 💫
• -c, --consistency REPS — use 0 <= REPS <= 5 (default: 2) passes of consistency transformation 🌀
• -ir, --iterative-refinement REPS — use 0 <= REPS <=1000 (default: 100) passes of iterative-refinement 🔁
• -pre, --pre-training REPS — use 0 <= REPS <= 20 (default: 0) rounds of pretraining 🏋️
• -pairs — generate all-pairs pairwise alignments 👯
• -viterbi — use Viterbi algorithm to generate all pairs (automatically enables -pairs) ⚡
• -v, --verbose — Report progress while aligning (default: off) 📢
• -annot FILENAME — write annotation for multiple alignment to FILENAME 📝
• -t, --train FILENAME — compute EM transition probabilities, store in FILENAME (default: no training) 🎓
• -e, --emissions — also reestimate emission probabilities (default: off) 🌟
• -p, --paramfile FILENAME — read parameters from FILENAME (default: ) 📂
• -a, --alignment-order — print sequences in alignment order rather than input order (default: off) 🔀

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🫶 SEE ALSO 🫶

• You can find more information in the manual of ProbCons, which is located in /usr/share/doc/probcons/manual.pdf in Debian systems. 📖
• An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE, probcons-RNA(1), is also distributed in the ProbCons Debian package. 🧪
• pc-makegnufile(1), pc-compare(1), pc-project(1), which are distributed separately in the probcons-extra package. 🧰

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📚 REFERENCE 📚

Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. 🎀 (yes bestie, cite the queens who built it)

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👑 AUTHORS 👑

• Chuong Do <chuongdo@cs.stanford.edu>
  • Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University. 🎓
• Charles Plessy <charles-debian-nospam@plessy.org>
  • Wrote this manpage in DocBook XML for the Debian distribution. 💖

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💜 COPYRIGHT 💜

This program and its manpage are in the public domain. 🌈 (free as in do whatever, bestie)

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and that's the whole vibe check, bestie — this was probcons 1.12, dated 2007-04-04, and it's the PROBCONS(1) page 🎀✨ mwah, go align some proteins 💅💖