Hi Malene, thanks for writing...
On Tue, 2010-11-30 at 04:09 +0100, Malene Bek-Thomsen wrote: > Hi Mauve users > > I’m a new user of Mauve and have problems aligning 50 bacterial genomes – a > mixture of complete genomes and incomplete genomes. It works very well with > the complete genomes, but the problem arrives when I want to add the > incomplete genomes consisting of multiple contigs. For each incomplete genome > I have downloaded a .gbff file from genbank containing all the contigs of > that genome in one file. I then thought I would be able to load the file into > Mauve and that Mauve would concatenate the contigs and align these incomplete > genomes with the complete genomes. However, when I add the incomplete genomes > in form of the .gbff file I end up with the following message: ERROR! gap > character encountered at genome sequence position 346579 Input sequences must > be unaligned and ungapped! Exited with error code: -1073741819. The gap > character found by Mauve seems to be the new entry –the beginning of the > next contig. I have looked at the .gbff file in text format and it looks as > expected for a genbank file. Can anyone tell me what I do wrong? > Glad to hear things are working well with your complete genomes. I believe the trouble you are encountering with the unfinished genomes might be related to the file name extension. Mauve uses file name extensions to guess the file format and only recognizes .gb and .gbk as genbank format. So if your .gbff files conform to the GenBank flat-file format well enough that Mauve can parse them, then renaming them to .gb or .gbk should solve the problem. If that doesn't solve it then please send me a sample of your data off-list so I can verify correct formatting. On a related note, I would highly recommend ordering the contigs in your draft genomes if you haven't already. Ideally that would be done with some kind of high resolution genetic map but if that's not available there are various software tools to order contigs based on reference genomes, including one in Mauve and written by Anna Rissman called the Mauve Contig Mover. GUI and command-line usage instructions are here: http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/reording-contigs-in-draft-genomes.html Other software tools for the task include Projector 2, Baccardi, OSLay, ABACAS, and probably more that I don't know about. I recommend ordering the contigs because it will allow progressiveMauve to run more efficiently (faster, less memory) and may even result in higher quality alignments. Cheers, -Aaron ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
