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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