RE-PCR(1)

💖 RE-PCR(1) — the reverse-search bestie 💖

okay so this is re-PCR, from the General Commands Manual section 1 — she's the one who finds sequence tagged sites in DNA sequences. group chat name: Reverse e-PCR. 🧬✨

✨ NAME ✨

re-PCR — find sequence tagged sites (STS) in DNA sequences 💅

🎀 SYNOPSIS 🎀

re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...]

re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-]
[-C batchcnt] [-o outfile] [-r+|-] [primers-file ...]

re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o
outfile] [-r+|-] [left right lo[-hi] [...]]

re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-]
[-C batchcnt] [-o outfile] [-r+|-] [stsfile ...]

four whole invocation moods, pick your fighter 🫶

🌸 DESCRIPTION 🌸

Okay bestie, listen. This one implements reverse searching — which, yes, is literally called Reverse e-PCR — and the whole point of that is to make it feasible to search the human genome sequence and other large genomes by doing STS and primer searches. big genome energy. no cap. 🔥

💅 OPTIONS 💅

• -p=hash-file — do a primer lookup using hash-file 🔍
• -P=hash-file — do a primer lookup using hash-file 🔍 (yes she's here twice, they're different flags, don't @ me)
• -s=hash-file — do an STS lookup using hash-file 🎯
• -S=hash-file — do an STS lookup using hash-file 🎯
• -n=mism — set the max allowed mismatches per primer for lookup 🧐
• -g=gaps — set the max allowed indels per primer for lookup 🕳️
• -m=margin — set variability for STS size for lookup 📏
• -l — use presize alignments (only if gaps>0) ⚠️ like literally only then
• -G — print alignments in comments 📝
• -d=min-max — set default STS size 📐
• -r=+|- — enable/disable reverse STS lookup 🔁
• -O=+|- — enable/disable syscall optimisation ⚡
• -C=batchcnt — set number of STSes per batch 🧺
• -o=outfile — set output file name 📁
• -q — quiet (no progress indicator) 🤫

also living in the synopsis rent-free: -h and -V. slay. 👑

🦋 EXAMPLE 🦋

here's the whole glow-up routine, step by step ✨:

famap -tN -b genome.famap org/chr_*.fa

fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap

re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200

See famap(1) and fahash(1) 🫶

🌈 SEE ALSO 🌈

• /usr/share/doc/ncbi-epcr/README.txt 📄
• bioperl(1), e-pcr(1), famap(1) and fahash(1) 🌟

💜 AUTHORS 💜

This manual page was written by 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 — dated April 2008, filed under RE-PCR(1), and honestly? iconic. go find those STSs. 💖✨🎀🦋