ECOPCR

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) 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

SEE ALSO

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