Find Chimeras - Frequently Asked Questions:
ES Wright et al. (2012) "DECIPHER, A Search-Based Approach to Chimera Identification for 16S rRNA Sequences." Applied and Environmental Microbiology, doi:10.1128/AEM.06516-11.
The sequence in the logo above is one of the first chimeras discovered using Find Chimeras. This sequence was classified as an Acidobacteria, but actually has parts belonging to the Actinobacteria and Bacteroidetes phyla.
DECIPHER’s FindChimeras function is a program that finds chimeras based on a search algorithm. Each sequence is evaluated by searching for and finding sets of short fragments that are uncommon in the phylogenetic group where the sequence is classified, but frequent in other phylogenetic groups. Find Chimeras is very simple to use. In brief, the user uploads their sequences in a FASTA-formatted text file and then receives the results as a tab-delimited text output file sent to their e-mail address.
Wrong entries are rejected immediately with an error message. The processing time depends on the number and length of the input sequences, as well as server load. Typical processing time is 1 - 6 hours for modest sequence sets, but can take as long as a week for a submission with hundreds of thousands of sequences.
Yes, submission of multiple files is permitted. Note that it typically takes much less time to process 1 set of 300 sequences than 10 sets of 30 sequences submitted sequentially. For this reason we encourage you to submit as many sequences at once as possible, so long as the file size is less than 50 MB. Please refrain from submitting more than four sequence files at a time.
The online Find Chimeras web-tool is only designed to work with 16S rRNA sequences. However, the DECIPHER stand-alone program can be configured to support 18S sequences. Please refer to the documentation available on the Documentation page or feel free to contact us for more information.