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ecoPCR - Online in the Cloud

Run ecoPCR in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command ecoPCR that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 formated 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 :

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

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