ECOPCR(1)

💖 ECOPCR(1) 💖

okay bestie, gather round — this is the manual page for ecoPCR, and yes, the man page name is literally ECOPCR(1). We're doing this. 🦋

✨ NAME ✨

ecoPCR — searching for sequence and taxonomy hybriding with given primers

🌸 SYNOPSIS 🌸

ecoPCR [options] <nucleotidic patterns>

🎀 DESCRIPTION 🎀

So like. ecoPCR is an electronic PCR software developed by LECA and Helix-Project. It helps to estimate Barcode primers quality. That's the whole vibe. It's giving "I do in silico PCR so you don't have to". 💅

👑 OPTIONS 👑

• -a — Salt concentration in M for Tm computation (default 0.05 M)
• -c — Consider that the database sequences are [c]ircular 🔄
• -d — [D]atabase : to match the expected format, the database has to be formatted first by the ecoPCRFormat(1) program. ecoPCRFormat(1) creates three file types:
  • .sdx : contains the sequences
  • .tdx : contains information concerning the taxonomy
  • .rdx : contains the taxonomy rank

ecoPCR needs all the file type. As a result, you have to write the database radical without any extension. For example /ecoPCRDB/gbmam

• -D — Keeps the specified number of nucleotides on each side of the in silico amplified sequences (including the amplified DNA fragment plus the two target sequences of the primers).
• -e — [E]rror : max errors allowed by oligonucleotide (0 by default)
• -h — [H]elp — print this help 🙈
• -i — [I]gnore the given taxonomy id. Taxonomy id are available using the ecofind program. see its help typing ecofind -h for more information.
• -k — [K]ingdom mode : set the kingdom mode — super kingdom mode by default. 👑
• -l — minimum [L]ength : define the minimum amplication length.
• -L — maximum [L]ength : define the maximum amplicationlength.
• -m — Salt correction method for Tm computation (SANTALUCIA : 1 or OWCZARZY:2, default=1)
• -r — [R]estricts the search to the given taxonomic id. Taxonomy id are available using the ecofind program. see its help typing ecofind -h for more information.
• first argument : oligonucleotide for direct strand
• second argument : oligonucleotide for reverse strand

📊 Table result description 📊

bestie the output table has 22 columns, and yes we're listing every single one because that's the assignment. 💖

• column 1 : accession number
• column 2 : sequence length
• column 3 : taxonomic id
• column 4 : rank
• column 5 : species taxonomic id
• column 6 : scientific name
• column 7 : genus taxonomic id
• column 8 : genus name
• column 9 : family taxonomic id
• column 10 : family name
• column 11 : super kingdom taxonomic id
• column 12 : super kingdom name
• column 13 : strand (direct or reverse)
• column 14 : first oligonucleotide
• column 15 : number of errors for the first strand
• column 16 : Tm for hybridization of primer 1 at this site
• column 17 : second oligonucleotide
• column 18 : number of errors for the second strand
• column 19 : Tm for hybridization of primer 1 at this site
• column 20 : amplification length
• column 21 : sequence
• column 22 : definition

🫶 SEE ALSO 🫶

http://www.grenoble.prabi.fr/trac/ecoPCR/

and that's the whole page, periodt ✨

kisses, this was ecoPCR version 0.5.0, dated June 2015 — iconic behavior honestly, go forth and amplify bestie 🧚💜🌸