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.