#49 Alignment errors or missing annotations when using gbk files from RefSeq

[Thomas Rattei]

Hi all,
at times we have problems when aligning or contig-moving sequences from NCBI refseq. Either the annotations do not show up, or the alignments entirely fails. We could switch to fasta format, but like the annotations to be displayed along the alignments.

Here is an example. The two files are attached, they are just downloaded from NCBI RefSeq. The error message of mauve:
...
Creating sorted mer list
ERROR! gap character encountered at genome sequence position 163
Input sequences must be unaligned and ungapped!
...

I was using the mauve snapshot 2015-02-25, installed from dmg file on the current MacOS.

Thanks for your help
Thomas