Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.
The chimera.slayer command identifies putative chimeras using the slayer approach.
ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences:
- the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera;
- candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence;
- the NAST alignment of the query sequence is improved in a 'chimera-aware' profile-based NAST realignment to the selected reference parent sequences; and
- an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences.
Note: It is not recommended to blindly discard all sequences flagged as chimeras. Some may represent naturally formed chimeras that do not represent PCR artifacts. Sequences flagged may warrant further investigation.