By a News Reporter-Staff News Editor at Life Science Weekly -- Current study results on DNA Research have been published. According to news reporting originating in Dresden, Germany, by NewsRx journalists, research stated, "High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track."
The news reporters obtained a quote from the research from the Dresden University of Technology, "This so-called multiplexing approach relies on a specific DNA tag or barcode that is attached to the sequencing or amplification primer and hence appears at the beginning of the sequence in every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and Levenshtein codes. Levenshtein codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this paper we demonstrate the decreased error correction capability of Levenshtein codes in a DNA context and suggest an adaptation of Levenshtein codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaption we take the DNA context into account and redefine the word length whenever an insertion or deletion is revealed. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors. We present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach."
According to the news reporters, the research concluded: "To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance."
For more information on this research see: Levenshtein error-correcting barcodes for multiplexed DNA sequencing. Bmc Bioinformatics, 2013;14():272. (BioMed Central - www.biomedcentral.com/; Bmc Bioinformatics - www.biomedcentral.com/bmcbioinformatics/)
Our news correspondents report that additional information may be obtained by contacting T. Buschmann, Institute for Medical Informatics and Biometry (IMB), Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Dresden, Germany (see also DNA Research).
Keywords for this news article include: Europe, Dresden, Germany, DNA Research.
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