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Chimera.ccode (version 1.39.5.0)

fasta - Candiate Aligned Sequences:

Select Reference Template from:

reference - Reference to align with:

filter - Apply a 50% soft vertical filter:

Mask option:

window - Length of sequence you want in each window analyzed:

Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length. Default is used if < 1

numwanted - Number of sequences compared with each query:

uses default if set to 0

Output logfile?:

Mothur Overview

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.

Command Documentation

The chimera.ccode command identifies putative chimeras using the ccode approach (Chimera and Cross-Over Detection and Evaluation). Ccode compares differences in distances, for each word, between query sequence and reference sequences, and reference sequences and themselves.

This method was written using the algorithms described in the paper "Evaluating putative chimeric sequences from PCR-amplified products" by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.

The program can analyze sequences for any required word length. Generally, values of 5-20% of sequence length appear to deliver accurate results, for example, working on 16S rDNA sequences with a full-length of #1500 nt. It should be noted that the use of fragments either too long or too short might result in a reduction of sensitivity.