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Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequencesDetection of chimeric artifacts formed when PCR is used to retrieve naturally occurring small-subunit (SSU) rRNA sequences may rely on demonstrating that different sequence domains have different phylogenetic affiliations. We evaluated the CHECK_CHIMERA method of the Ribosomal Database Project and another method which we developed, both based on determining nearest neighbors of different sequence domains, for their ability to discern artificially generated SSU rRNA chimeras from authentic Ribosomal Database Project sequences. The reliability of both methods decreases when the parental sequences which contribute to chimera formation are more than 82 to 84% similar. Detection is also complicated by the occurrence of authentic SSU rRNA sequences that behave like chimeras. We developed a naive statistical test based on CHECK_CHIMERA output and used it to evaluate previously reported SSU rRNA chimeras. Application of this test also suggests that chimeras might be formed by retrieving SSU rRNAs as cDNA. The amount of uncertainty associated with nearest-neighbor analyses indicates that such tests alone are insufficient and that better methods are needed.
Document ID
20050000214
Acquisition Source
Legacy CDMS
Document Type
Reprint (Version printed in journal)
Authors
Robison-Cox, J. F.
(Montana State University Bozeman 59717, United States)
Bateson, M. M.
Ward, D. M.
Date Acquired
August 22, 2013
Publication Date
April 1, 1995
Publication Information
Publication: Applied and environmental microbiology
Volume: 61
Issue: 4
ISSN: 0099-2240
Subject Category
Life Sciences (General)
Distribution Limits
Public
Copyright
Other
Keywords
NASA Discipline Exobiology
Non-NASA Center

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