![]() This can happen when a chimeric insert (an insert assembled from several separate pieces of DNA) is sequenced or when multiple contaminated sequences are assembled into a longer sequence. Occasionally, however, foreign DNA segments can be found in the middle of a query sequence. Foreign sequences are therefore much more commonly found near the ends of a query. Although weak matches often occur by chance, they indicate foreign sequence whenever there is corroborating evidence of contamination.Īdapters, linkers, PCR primers, and vectors are all attached to the ends of the source DNA/RNA. Weak matches identify sequence segments that are potentially of foreign origin. Sometimes, however, there is a valid reason why part of the query sequence should match a sequence in the UniVec database (see Exceptions). The occasional moderate match that occurs by chance will lack any corroborating evidence of contamination. ![]() Consequently, strong and moderate matches usually indicate that the segment originated from foreign DNA (vector, adapter, linker, or primer) that was attached to the source DNA/RNA during the cloning process. ContaminationĪ query sequence containing one or more segments of foreign sequence is said to be contaminated because the foreign sequence does not represent the genetic information from the biological source organism.īy definition, strong matches very rarely occur by chance, and moderate matches rarely occur by chance. Foreign DNAĪny DNA that does not originate from the biological source organism. Sequence representing the genetic information from the biological source organism. genomic DNA or mRNA, from the biological source organism being studied. How to Relate a UniVec Database Segment to Its Parent Sequence.Removing Internal Segments of Foreign Sequence Removing Terminal Segments of Foreign Sequence Identifying the Boundaries of the Foreign Sequence.When VecScreen May Underestimate the Extent or Significance of Contamination This document provides guidance for evaluating the significance of matches reported by VecScreen and also for decontaminating the query by removing the foreign sequences. The origin of such segments should be questioned because they are likely to have been derived from foreign DNA. The VecScreen output lists all segments of the query sequence that closely match any of the sequences in the UniVec database.
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