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Chimera check your aligned sequences.
Use this tool to check a set of NAST-aligned 16S rRNA gene sequneces for chimeras using Bellerophon. A fasta file of your non-chimeric sequences will be sent by email along with a spreadsheet of results. This is a beta tool, so please provide feedback.

Known Issues:

Please make sure there are no spaces or other "odd" characters in your file names.
Remove any parenthesis from the sequence IDs in your fasta file, and xls file. Consider using a Find-Replace tool.

Also, a few bugs still exist so some jobs do not complete and no email will be sent.
You may want to contact Todd before you submit a job for testing.

My aligned fasta formatted sequence file:
Be sure that your file is fasta formatted.
My NAST summary table:
Be sure that this table is saved as tab delimited text.
My parameter file: (Optional for advanced users. See sample.)

Parameters:

Compare your sequences to each other. (Must be CHECKED)
Compare your sequences to Core Set (Be sure your alignment is in 7682 character format if you use this option).

Similarity to Core Set sequence threshold:
Match length to Core Set sequence threshold:
Sequences with above threshold BLAST similarity and BLAST length will be considerd non-chimeric and divergent parental searches will be skipped.

Window size (sequences will need to have enough non-masked bases to span 2 windows to be evaluated):

Count of similar sequences to search for each window:

Disregard hyper-variable regions by using lane mask. (Be sure your alignment is in 7682 character format if you use this option).


parent-to-fragment threshold:
Fragments which cannot find potential parents with similarity above this threshold will not be considerd to be matches to the parent.



Divergence ratio threshold:
Set the ratio which must be exceeded to determine if parent-fragment relationships denote a putative chimera.



Email address to send results (required):


Submit request.
 
  • Last Database Update: October 2, 2011 1:41PM
  • 1049116 aligned 16S rDNA records >1250nt