Chimera Detection Analysis Command FAQ
Overview
This FAQ contains information related to using the online Chimera Detection Analysis Command function. Please direct all corrections and additions to RDP-II General Support (rdpstaff@msu.edu). This FAQ can be found on the Web at http://www.cme.msu.edu/RDP/docs/chimera_faq.html. Information in this FAQ is primarily based on e-mail received via the RDP-II Support page linked at the bottom of the analysis form.
    Frequently Asked Questions
  1. Q: What does Chimera Detection do?
    A: Chimera Detection looks at the number of unique oligomers in common between the unknown sequence and the most similar database sequence. It generates a histogram to visually indicate a hypothetical break-point in your sequence that would split your unknown sequence into two fragments that are of chimeric origin.

  2. Q: Is this possible to study possible chimeric sequences in our own database of sequences and exclude the RDP database? Our partial sequences are approximately 450 nucleotides long.
    A: It is possible to compare your sequences to each other and to the sequences in the RDP dataset at the same time, but the RDP dataset can't be excluded. When pasting your sequences in, be sure to paste them in both boxes - the "sequence upload" and the "expand RDP" boxes. For ease of interpretation, have the results emailed to you. Using a test set of closely related sequences not found in the RDP dataset, we found that the top twenty matches for most of the sequences had, at most, two or three RDP sequences as matches.

    We would urge you to go on to use secondary structure, signature analysis and "breaking and retreeing" analyses to confirm or refute the Chimera Detection results. Unfortunately, your sequences are of a length that renders some of these methods useless, depending on the region of the molecule you have sequenced. For example, a secondary structure analysis of the first 400 bases of a typical 16S rDNA sequence only includes base pairs formed between local portions of the molecule and thus will only detect chimeras formed within this relatively small region. The only cure for these problems is more data.

    Two pieces of software available from the RDP that will be helpful in your phylogenetic analyses: fastDNAml and DNArates. These are UNIX programs, although a version of fastDNAml compiled for Macintosh is available as part of SeqPup from Don Gilbert at Indiana.




 Last updated on 08/30/1999.