Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

By Thomas Huber, G. Faulkner, Philip Hugenholtz. Bioinform., 2004

1,629 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/229c92fd7c8248c8eff0f6ea04f4b256bd89a66b

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Citations in the corpus

Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils (2014, methodology): “7 (Ann Arbor, MI, USA) and potential chimeric sequences were identified and discarded using the Bellerophon software (Huber et al., 2004).”
Ecology and exploration of the rare biosphere (2015, methodology): “Software for chimaera detection 171,172 and modelling sequencing noise 173 , and methods to reduce inflated richness estimates 35 , have increased confidence in the validity of OTUs resulting from HTS surveys.”
Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota (2007, methodology): “The files were then tested for the presence of chimeric sequences using Mallard [52] and Bellerophon [55], and putative chimeras were checked using Pintail [56] and BLAST [57].”
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes (2006, background): “The resulting ‘Core Set’ of 10 270 aligned records were non-chimeric (13) and >1250 nt in length.”
Characterization of Gut-Associated Bacteria in Larvae and Adults of the Southern Pine Beetle, Dendroctonus frontalis Zimmermann (2006, methodology): “Clone sequences were tested for chimeric structures by using RDP Check_Chimera (Cole et al. 2005) and Bellepheron ( Huber et al. 2004 ), and chimeras were excluded from further analyses.”
Bacteria Associated with the Guts of Two Wood-Boring Beetles: Anoplophora glabripennis and Saperda vestita (Cerambycidae) (2006, methodology): “Putative chimeras were identiÞed by using CHECK CHIMERA (Cole et al. 2005), helical base pairing, and partial treeing (Huber et al. 2004).”
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. (2011, background): “sequence quality and contain few to more than 45% chimeric sequences (Huber et al. 2004; Ashelford et al. 2005, 2006; Quince et al. 2009).”
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing (2008, methodology): “Full-length amplicons were cloned and sequenced with Sanger dideoxy methods, assembled with phrap [36], aligned with NAST [31] and evaluated for chimeras with Bellerophon [37] (GenBank Accession numbers: EU761594-EU768801).”