articleApplied and Environmental MicrobiologyNov 19, 2011BRONZE OA

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

ESErik S. WrightLŞL. Şafak YılmazDRDaniel R. Noguera

University of Wisconsin–Madison

PubMed
Indexed incrossrefdoajpubmed

Abstract

DECIPHER is a new method for finding 16S rRNA chimeric sequences by the use of a search-based approach. The method is based upon detecting short fragments that are uncommon in the phylogenetic group where a query sequence is classified but frequently found in another phylogenetic group. The algorithm was calibrated for full sequences (fs_DECIPHER) and short sequences (ss_DECIPHER) and benchmarked against WigeoN (Pintail), ChimeraSlayer, and Uchime using artificially generated chimeras. Overall, ss_DECIPHER and Uchime provided the highest chimera detection for sequences 100 to 600 nucleotides long (79% and 81%, respectively), but Uchime's performance deteriorated for longer sequences, while ss_DECIPHER…

Citation impact

725
total citations
FWCI
17.03
Percentile
100%
References
17
Citations per year

Authors

3

Topics & keywords

Topics
Keywords
  • DECIPHER
  • Chimera (genetics)
  • Computational biology
  • Phylogenetic tree
  • Biology
  • Phylogenetics
  • Genetics
  • Gene
No related works found for this paper.

Funding