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Clustal Omega alignment does not complete and results in a “fatal error” message

Clustal Omega alignment does not complete and results in a “fatal error” message

Clustal Omega alignment does not complete and results in a “fatal error” message

June 17, 2014 Product Notifications

Date:   6/17/2014

 

Version Affected:  11.2 and higher

 

Version Fixed:  N/A

 

Issue:  Clustal Omega requires that each sequence in an alignment contain at least one residue that is not an ambiguity code.

 

Resolution:

 

  • DNA sequences must contain at least one A, C, T or G.
  • RNA sequences must contain at least one A, C, U, or G.
  • Protein sequences must contain at least one A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W or Y.

 

If there are any sequences that do not meet this requirement, Clustal Omega will terminate with a “fatal error” message (visible in the MegAlign Pro Console), and no alignment will be created.

 

To address this issue, you can do either of the following:

 

  • Remove the sequence and try aligning again with Clustal Omega.
  • Include the sequence, but switch to MAFFT or MUSCLE as the alignment method. Neither of these algorithms requires sequences to contain at least one non-ambiguous residue.

 

If you have any questions about this issue, please contact DNASTAR by calling 866-511-5090 or by e-mailing us at support@dnastar.com.

 

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