NTDPAL(1)

💖 NTDPAL(1) — like, the whole entire manual 💖

okay bestie, sit down, hydrate, because we're about to talk about ntdpal, from the Primer3 User Manuals family. she's a whole icon and she deserves your full attention. 🫶

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✨ NAME ✨

ntdpal — bestie, this is the one that provides Primer3's alignment functionality. that's literally her whole job and she ate. 💅

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🌸 SYNOPSIS 🌸

here's the vibe check, the summoning ritual, the exact way you call her up:

ntdpal [-g gval] [-l lval] [-m mval] [-f1, f2, f3] [-p] [-s] [-e] {seq1}
       {seq2} {mode}

no cap, that's it. two sequences, one mode, some flags if you're feeling fancy. 🦋

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🧚 DESCRIPTION 🧚

so Ntdpal stands for NucleoTide Dynamic Programming ALignment (yes she has a government name) and she is a stand-alone program that hands you Primer3's alignment functionality. we're talking:

• local alignment, a.k.a. Smith-Waterman
• global alignment, a.k.a. Needleman-Wunsch
• plus the extra mysterious one, "half global" 👑

three flavours, one queen. periodt.

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💅 OPTIONS 💅

this is the part where we go through every single flag because we do not skip content in this house. every one of them, bestie. let's go. 🎀

• -g gval — gval is a (positive) float with .01 precision, and it sets the penalty for creating a gap. heads up: the penalties get subtracted from the output score, so yeah, it's giving consequences. 😭
• -l val — lval is a (positive) float with .01 precision, and it's the penalty for lengthening a gap. and same deal — those penalties are subtracted from the output score. she's strict but fair. ✨
• -a — this one causes the scoring matrix to be modified by dpal_set_ambiguity_codes. letting the ambiguity codes in, love that for her. 🦋
• -e — causes the end position of the alignment in both sequences to be printed. and do NOT confuse this with the 'e' mode, bestie, they are two completely different girlies. 🙈
• -f1, -f2, -f3 — these force specific implementations. and -f2? she forces use of an implementation that might provide more informative error messages, possibly at the expense of some speed. trade-offs, we love a trade-off. 💀
• -h — use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = -0.5. for context, the default scoring matrix assigns 1 to a match and -1 to a mismatch. glow-up matrix, honestly. ⭐
• -p — causes the alignment to be displayed on stderr. that's it, that's the whole thing. dramatic entrance, love it. 🌈
• -s — causes only the score to be printed. minimalism, main character energy, no extra commentary. 👑
• -m mval — mval is the maximum allowed gap, and the default is 3. know your limits, bestie. 🍓
• seq1 and seq2 — these are the sequences to be aligned. the two little guys. the whole point. 💜
• mode — okay this is the important one, it's one of g, G, l, or L, specifying a:
  • g — global alignment
  • G — global end-anchored alignment
  • l — local alignment
  • L — local end-anchored alignment

and for backward compatibility, e is equivalent to G. keeping the old letters alive, we respect the elders. 🫶

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📚 REFERENCE 📚

please cite, bestie, it's the least we can do:

Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386.

academic girlies stay winning. 🎓✨

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👀 SEE ALSO 👀

go read these too, iykyk:

• primer3_core(1)
• oligotm(1)

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💖 COPYRIGHT 💖

Copyright © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky

All rights reserved. on Debian-based systems, please consult /usr/share/doc/primer3/copyright to read the licence of ntdpal. fr fr, go check it, don't just vibe past the legal stuff. 🙈

this manual page was written by Charles Plessy <plessy@debian.org> for the Debian(TM) system (but may be used by others — she's generous like that 💅). permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself.

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and that's the whole page, bestie!! 🌈💖✨

this was ntdpal 1.1.4, dated 11/30/2011 — written down in the Primer3 User Manuals, and now explained to you in a group chat. no cap, you're basically a nucleotide alignment expert now. go forth and align. 🦋👑🎀💜