Question: MAUVE: No gene annotations in Genbank file alignments
0
gravatar for tptacek3050
4.3 years ago by
tptacek305060
United States
tptacek305060 wrote:

I'm trying to align 15 genbank files generated by RAST for 15 Mycoplasma genomes that we have assembled. I am aligning the files with progressivemauve with default parameters, and visualizing with MAUVE's GUI. The alignment runs fine, but when I visualize it, I get "(no annotations loaded)" for each genome. I've tried this using a genbank file for a reference Mycoplasma genome and I get the same result.

Has anyone run into the problem before and/or does anyone have any suggestions?

ADD COMMENTlink modified 3.9 years ago by izwanspp10 • written 4.3 years ago by tptacek305060
1
gravatar for izwanspp
3.9 years ago by
izwanspp10
United States
izwanspp10 wrote:

I've had the same problem recently. It helps if you go through the Mauve_console, as it will mention what type of error has occurred during the run.

In my recent run for example, the console printed out a "locus line too short" error. So, in which case I simply edited the *.genbank file's information in the LOCUS row; shortening the identifier (the sample ID located to the immediate right of the "LOCUS" tag). I'm not sure exactly why, but perhaps a lengthy identifier messes with the tab delimited format, resulting in MAUVE being unable to read the file properly.

ADD COMMENTlink written 3.9 years ago by izwanspp10

I just deleted the redundant gaps in the LOCUS row, then annotation loading worked! 

ADD REPLYlink written 3.6 years ago by yolandaly0
0
gravatar for tptacek3050
4.3 years ago by
tptacek305060
United States
tptacek305060 wrote:

Just bumping this up in case anyone knows anything.

ADD COMMENTlink written 4.3 years ago by tptacek305060
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