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/