E-PCR(1)

💖 E-PCR 💖

okay bestie, listen up — this is the manual page for e-PCR, a General Commands Manual situation, and we're gonna get you fluent in it. No cap. ✨

✨ NAME ✨

e-PCR — find sequence tagged sites (STS) in DNA sequences 🧬🦋

🌸 SYNOPSIS 🌸

e-PCR [-hV] [posix-options] stsfile [fasta ...] [compat-options]

Like… that's the whole vibe. <pink>stsfile</pink> is required, the fasta files are the entourage, and everything else is optional garnish. 💅

🎀 DESCRIPTION 🎀

So basically, this program substitutes blast in the location of pairs of primers on the genome that may yield a PCR product. That's it, that's the whole thing. It's giving primer-pair-finder, main character energy, and it ate. 🔥

💅 OPTIONS 💅

posix-options

• -m=## — Margin (default 50)
• -w=## — Wordsize (default 7)
• -n=## — Max mismatches allowed (default 0)
• -g=## — Max indels allowed (default 0)
• -f=## — Use ## disontiguous words, slow if ##>1 🐌
• -o=## — Set output file
• -t=## — Set output format:
  • 1 — classic, range (pos1..pos2)
  • 2 — classic, midpoint
  • 3 — tabular
  • 4 — tabular with alignment in comments (slow) 🐢
• -d=##-## — Set default size range (default 100-350)
• -p=+- — Turn hits postprocess on/off
• -v=## — Verbosity flags
• -a=a|f — Use presize alignments (only if gaps>0), slow
  • a — Always, or f — as Fallback
• -x=+- — Use 5'-end lowercase masking of primers (default -)
• -u=+- — Uppercase all primers (default -)

compat-options

Not me explaining that these are literally duplicates of the posix-options. Same energy, different outfit. 👯

• M=## — Margin (default 50)
• W=## — Wordsize (default 7)
• N=## — Number of mismatches allowed (default 0)
• G=## — Max indels allowed (default 0)
• F=## — Use ## discontinuous words
• O=## — Set output file to ##
• T=## — Set output format (1..3)
• D=##-## — Set default size range
• P=+- — Postprocess hits on/off
• V=## — Verbosity flags
• A=a|f — Use presize alignments (only if gaps>0), slow
  • a — Always, or f — as Fallback
• X=+- — Use 5'-end lowercase masking of primers (default -)
• U=+- — Uppercase all primers (default -)
• -mid — Same as T=2

For information about further options just call e-PCR without any options. (yes really, just run it bare and let it yap 🗣️✨)

🦋 SEE ALSO 🦋

• /usr/share/doc/ncbi-epcr/README.txt
• bioperl(1), re-pcr(1)

👑 AUTHORS 👑

This manual page was written by Steffen Moeller <moeller@debian.org> and Andreas Tille <tille@debian.org> for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.

On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

and that's the whole page, bestie 💖✨🎀

This one's dated February 2004 and it ships as E-PCR(1) in the General Commands Manual — so like, ancient lore, but we understood it, we ate, we left no crumbs. 🫶🌸👑