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Mitochondrial DNA is most commonly used, e.g., for species identification ("DNA barcoding").
Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking.
However, in our experience the main costs for barcoding relate to sample acquisition and processing (identification, DNA extraction), which are one-time costs that depend on the salaries of expert personnel.
This study compares three genetic markers (16S, cyt b, and COI) used as identification tools to distinguish 50 fish species common in European seas in terms of (1) their power of resolution in sequence-based species identification (DNA barcoding) and (2) their applicability in oligonucleotide probe design for the development of a low density DNA microarray.
After tick identification, DNA was extracted from ticks by using QIAmp DNeasy kits (QIAGEN, Hilden, Germany).
For molecular identification, DNA was PCR amplified using universal primers ITS1 and ITS4 [ 54].
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After eliminating: i) incomplete reads, ii) twin-ditags, and iii) ditags without complete library-identification DNA linkers, a total of 330,000 26 bp tags were obtained for further analysis.
The total number of SuperSAGE tags obtained after sequencing the libraries in a single 454 plate and eliminating i) incomplete reads, ii) twin-ditags, and iii) ditags without complete library-identification DNA linkers was 354,930; comprising 227,536 tags from the wounding (W) library and 127,394 from the FAC-elicited (F) library (Table 1).
To optimize correct identifications, DNA sequences of four candidate regions (rbcL, matK, ITS2, psbA- trnH) from non- Camellia tea were determined from the best reciprocal hits.
To establish statistical significance, each DNA-based identification (or DNA fingerprint) uses DNA fragments from several marker sites.
This approach allows the identification of DNA binding sites of any DNA-associated protein.
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