---
name: "ecoPCR"
section: "1"
platform: "linux"
package: "ecopcr"
version: "1.0.1+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ecoPCR"
---

# ecoPCR(1)

searching for sequence and taxonomy hybriding with given primers

## NAME

ecoPCR - searching for sequence and taxonomy hybriding with given primers

## SYNOPSIS

**ecoPCR** **\[options\]** *\<nucleotidic patterns\>*

## DESCRIPTION

ecoPCR is an electronic PCR software developed by LECA and Helix-Project. It helps to estimate Barcode primers quality.

## 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)](/ecoPCRFormat/1.md) program. [ecoPCRFormat(1)](/ecoPCRFormat/1.md) 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 :

  - 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/