title: Oligonucleotide frequencies of barcoding loci can discriminate species across kingdoms.
abstract: BACKGROUND
  DNA barcoding refers to the use of short DNA sequences for rapid identification of species. Genetic distance or character attributes of a particular barcode locus discriminate the species. We report an efficient approach to analyze short sequence data for discrimination between species.
  
  
  RESULTS
  A new approach, Oligonucleotide Frequency Range (OFR) of barcode loci for species discrimination is proposed. OFR of the loci that discriminates between species was characteristic of a species, i.e., the maxima and minima within a species did not overlap with that of other species. We compared the species resolution ability of different barcode loci using p-distance, Euclidean distance of oligonucleotide frequencies, nucleotide-character based approach and OFR method. The species resolution by OFR was either higher or comparable to the other methods. A short fragment of 126 bp of internal transcribed spacer region in ribosomal RNA gene was sufficient to discriminate a majority of the species using OFR.
  
  
  CONCLUSIONS
  Oligonucleotide frequency range of a barcode locus can discriminate between species. Ability to discriminate species using very short DNA fragments may have wider applications in forensic and conservation studies.
authors.affiliation: Center for Plant Molecular Biology, National Botanical Research Institute, Council of Scientific and Industrial Research, Lucknow, India.
authors.forename: Antariksh
authors.initials: A
authors.lastname: Tyagi
authors.forename: Sumit K
authors.initials: SK
authors.lastname: Bag
authors.forename: Virendra
authors.initials: V
authors.lastname: Shukla
authors.forename: Sribash
authors.initials: S
authors.lastname: Roy
authors.forename: Rakesh
authors.initials: R
authors.lastname: Tuli
mesh_terms: D000818:Animals; D016172:DNA Fingerprinting / Q000379:methods*; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005658:Fungi / Q000145:classification / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics*; D054643:INDEL Mutation; D020407:Internet; D009838:Oligodeoxyribonucleotides / Q000235:genetics*; D010802:Phylogeny; D010944:Plants / Q000145:classification / Q000235:genetics; D013045:Species Specificity
chemical_list: D021903:DNA, Ribosomal Spacer; D009838:Oligodeoxyribonucleotides
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