PRIMER3_CORE(1)

📦
version 2.6.1 · 2 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 primer3_core — the manual, but make it make sense 💖

okay bestie, welcome to PRIMER3_CORE, from the Primer3 User Manuals situation. This is your girl for designing primers for PCR. Let's get into it 💅

🌸 NAME 🌸

primer3_core — Designs primers for PCR 🧬✨

💫 SYNOPSIS 💫

primer3_core [-format_output] [-strict_tags] [< input_file]

lowkey that's the whole vibe right there 🫶

🦋 DESCRIPTION 🦋

So primer3_core picks primers for PCR reactions, and it's obsessed with criteria, ok? It considers:

  • oligonucleotide melting temperature
  • size
  • GC content
  • primer-dimer possibilities
  • PCR product size
  • positional constraints within the source sequence
  • and miscellaneous other constraints (yes, "miscellaneous", it said what it said)

By default, primer3_core accepts input and produces output in Boulder-io format — that's a pre-XML, text-based input/output format for program-to-program data interchange. The Boulder-io format and the commands that primer3_core understands are described in the README file, which on Debian systems can be found in /usr/share/doc/primer3/. go read it, it's giving required reading 📖✨

✨ OPTIONS ✨

  • -format_output — prints a more user-oriented report for each sequence. like, readable-readable, not just machine-readable 😌
  • -strict_tags — so by default primer3_core echoes and ignores any tags it does not recognize. but if the -strict_tags flag is set on the command line, primer3_core prints an error in the PRIMER_ERROR output tag, and also prints additional information on stdout. this option can be useful for debugging systems that incorporate primer. very much a "who dis" energy 🕵️♀️
Note 📌 The old flag -2x_compat is no longer supported. she's gone. rest in peace bestie 💀🚫

🔥 EXIT STATUS CODES 🔥

know your numbers, they're telling you something:

  • 0 on normal operation. slay, she's fine 💖
  • -1 under the following conditions: illegal command-line arguments, unable to fflush stdout, unable to open (for writing and creating) a .for, .rev or .int file (probably due to a protection problem). 😭
  • -2 on out-of-memory. brain empty, no thoughts 💀
  • -3 empty input. she needed something to work with 🥺
  • -4 error in a "Global" input tag (message in PRIMER_ERROR). 🙈

📚 REFERENCE 📚

Please cite — yes please, citation is not optional bestie, it's giving academic main character energy 👑:

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.

👀 SEE ALSO 👀

(the friends of the family 💞)

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 primer3_core. like, actually read it, fr fr 📜

This manual page was written by Steffen Moeller <moeller@debian.org> for the Debian(TM) system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the same terms as primer3_core itself.

aaaand that's the page, bestie 🎀 she's primer3_core 1.1.4, dated 05/09/2008 — iconic, historic, still running. no cap. byeeee 🦋💖✨

📦 where this page comes from