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ecoPCR specifications

Information


Unique identifier OMICS_19861
Name ecoPCR
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License CeCILL version 2.1
Computer skills Advanced
Version 0.8.0
Stability Stable
Maintained No

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http://metabarcoding.org/obitools/doc/scripts/ecoPCR.html

ecoPCR in publications

 (33)
PMCID: 5931749
PMID: 29732403
DOI: 10.1126/sciadv.aap9661

[…] to add homologous sequences from other non-elasmobranch taxa, an in silico pcr was performed against release r117 of the embl-ebi database using ecopcr (). subsequently, the obtained reference sequences were added to the elasmobranch sequences obtained from bold. these additional reference sequences were added to our elasmobranch database […]

PMCID: 5845510
PMID: 29535774
DOI: 10.1155/2018/6169546

[…] and 70°c for 10 min., relative quantification of gene expression levels for transforming growth factor-β1 (tgfb1) and apelin (apln) genes was carried out by real-time quantitative pcr (rt-pcr) on ecopcr real-time system (illumina, san diego, ca, usa) using cdna samples obtained as described before. for this purpose, sybr® select master mix (thermo fisher scientific, waltham, ma, usa) was used […]

PMCID: 5792609
PMID: 29435248
DOI: 10.1002/ece3.3791

[…] amplicons were then ligated to illumina adaptors, and hts was carried out on miseq 2000 150pe (illumina inc., usa)., reference databases of chloroplast trnl intron of plants were assembled using the ecopcr program (ficetola et al., ) and sequences derived from public databases (national center for biotechnology information, ncbi; european molecular biology laboratory, embl; dna data bank […]

PMCID: 5715122
PMID: 29203793
DOI: 10.1038/s41598-017-17150-2

[…] that included our 127 bp target fragment. in order to add homologous sequences from other, non-elasmobranch taxa, an in silico pcr was performed against release r117 of the embl-ebi database using ecopcr. subsequently, the obtained reference sequences were added to the elasmobranch sequences obtained from bold. these additional reference sequences were added to our elasmobranch database […]

PMCID: 5686199
PMID: 29138485
DOI: 10.1038/s41598-017-15375-9

[…] sequence reads over the whole data set. motu identification was done using the ecotag algorithm, the reference database was constituted from the embl nucleotide sequence database release 126 using ecopcr., we estimated alpha diversity for 16s rrna and trnl data using the shannon diversity index. we tested for significant effects of categorical metadata for alpha diversity using […]

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