![]() Adaptors are frequently used in the construction of cDNA libraries and in generating cDNA ends using rapid amplification of cDNA ends (RACE) PCR. Usually adaptors consist of several restriction sites, one blunt end (for ligation to cDNA) and one cohesive end (for ligation to a vector). Strategies to decrease contamination in database sequences have emphasized vector sequences ( 4–6, 8) and given little attention to adaptor contamination.Īn adaptor is a short oligonucleotide that is ligated to the ends of cDNAs for incorporation into a vector cloning site ( Figure 1). There is one published account of contamination due to adaptor sequences, where it was shown that commercial adaptor sequences matched the 5′ or 3′ end of 728 GenBank and the European Molecular Biology Laboratory (EMBL) sequences ( 13). Sources of contamination for nuclear DNA and cDNA include vector sequence ( 1–6), plasmid vector insertion sequences ( 7), impure tissue sources ( 8), faulty laboratory protocols ( 9, 10), mitochondrial DNA ( 11), and ribosomal DNA/RNA ( 12). More than 99% of sequences contaminated with adaptors fall into one of the three groups shown at the bottom.Ī contaminated sequence is defined as “one that does not faithfully represent the genetic information from the biological source organism/organelle because it contains one or more sequence segments of foreign origin” ( ). The path from sequencing a cDNA to an improperly edited sequence. Awareness that over 99% of adaptor contaminants appear near the ends of sequences, are flanked by a vector, or involve adaptor dimerization allows the detection of 99% of these sequences ( Figure 1). Here we describe a simple screen that identified adaptor contamination in over 78,000 eukaryotic sequences in GenBank ®. Analysis of DNA sequences can only be as correct as the sequences themselves, and so contamination in public databases is a major concern for bioinformatics research.
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