table of contents
ECOPCR(1) | User Commands | ECOPCR(1) |
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¶
June 2015 | ecoPCR 0.5.0 |