Hi Alina, Mauve is notoriously picky about input file formats. But that said, I just downloaded a couple of bacterial genomes via the route you described (not the route I normally use), and they were aligned without any problem.
As to getting the sequences via ftp, it has been so long since I set my system up to use a dedicated ftp client instead of a web browser for ftp that I don't remember the procedure. But I think you can right-click on a filename to download the file. For complete genome sequences in FASTA format you want the one with .fna as the extension. If you want to send me one of your problem files, I could take a look at it ... no promises, but I might just notice something. Guy Dr. Guy Plunkett III Senior Scientist, Genome Center of Wisconsin Senior Scientist, DNASTAR http://www.genome.wisc.edu/information/gplunkett.html On 9/5/12, Alina Grigorescu wrote: >Hi everybody, > > >I am trying to run Mauve (in Windows) to compare a de novo assembly with >already published genomes of the same bacterial genus and each time I start an >alignment, Mauve stops working after a short while and gives some error code >(most often 255). > > >I believe there is a problem with the input files but I can't figure out which. > > >I also tried a test run only with genome sequences downloaded from NCBI but >the test was unsuccessful as well. My conclusion is that perhaps I don't >download the correct files. > > >So to download genome sequence files, I looked for the organism of interest in >the "Genome" database from NCBI, then I selected the "Graphics" view, then >"Tools">"download">"FASTA". Apparently Mauve did not like the files I got. > >I also tried to go on the NCBI FTP site, but there is no option of "download" >files. When clicking on a file, a new webpage opens with sequence information. >So I tried to copy all the sequence information displayed on the webpage and >paste it in a .txt file, then use the .txt file for Mauve alignments. Mauve >stopped working. > > >Could anybody please explain me how should I obtain correct genome sequences >and file formats that would work with Mauve? Moreover, I would like to know >how to get the annotated genome sequences. > > >Thanks, > >Alina > > >-- > >Alina Grigorescu, PhD ><mailto:[email protected]>[email protected] ><mailto:[email protected]>[email protected] > >Postodctoral Researcher >Centre Wallon de Biologie Industrielle >Universite de Liege >Sart-Tilman, B40 >Tel: +3243663997 > > >------------------------------------------------------------------------------ >Live Security Virtual Conference >Exclusive live event will cover all the ways today's security and >threat landscape has changed and how IT managers can respond. Discussions >will include endpoint security, mobile security and the latest in malware >threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > >_______________________________________________ >Mauve-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
