Hi Cristina, Mauve uses a GenBank sequence file parser implemented in BioJava 1.7, which is somewhat strict & brittle in its interpretation of the format. If you can provide the error messages that appear in the Mauve console log when you load the alignment then myself or someone else on the list might be able to suggest how to modify the genbank files so they are palatable to BioJava (and Mauve).
Best, -Aaron On Fri, 2014-07-18 at 11:25 +1000, cav00...@nodai.ac.jp wrote: > Dear mauve-users support, > > My knowledge in Bioinformatics are rather limited, but I was familiar > with MAUVE because I used it during my PhD a few years ago. I used to > perform progressive alignments of multiple drag genomes by using embl (. > embl) or genbank (.bg or .gbk) files as input and I obtained a nice > alignment and was able to find the topology of interesting genes. > > But now, since I started to study a new set of genomes, using draft > genomes in genbank format (.gbk) as input data in MAUVE, I get an > alignment as output, but I also encounter the problem that annotations > are not loaded. > > I will really appreciate if you could guide me a little bit in finding > the source of this problem. > > Thank you very much in advance and best regards. > > Cristina > ------------------------ > Cristina Andres-Barrao, PhD. > cav00...@nodai.ac.jp > Laboratory of Fermentation Biochemistry > Department of Fermentation Sciences > Faculty of Applied Biosciences > Tokyo University of Agriculture > 1-1-1 Sakuragaoka, Setagaya-ku > Tokyo 156-8502, Japan > > > > ------------------------------------------------------------------------------ > Want fast and easy access to all the code in your enterprise? Index and > search up to 200,000 lines of code with a free copy of Black Duck > Code Sight - the same software that powers the world's largest code > search on Ohloh, the Black Duck Open Hub! Try it now. > http://p.sf.net/sfu/bds > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
