Hello. While mauve doesn't produce output in the format you suggest, this information shouldn't be hard to reconstruct. In each alignment directory produced by the Mauve Contig Mover run, there will be a file with a name ending with "_contigs.tab". This file includes information about the contigs. In particular, the section labeled "Ordered Contigs" (this may be the only section in the file) contains the contigs in the order they were in that alignment with coordinates. The "_contigs.tab" file in the "alignment1" directory will contain the original coordinates, and the file in the highest numbered alignment directory will contain the final order and coordinates. This section of these files can be easily loaded into Microsoft Access, or R, or a scripting language, and it shouldn't be hard to match up original to final order. Hope that helps! Anna On 09/11/12, "Münsterkötter, Martin, Dr." wrote: > > Hi > > Mauve concatenates chromosomes (contigs) prior to alignment. > > How can this concatenates coordinates in an mauve alignment mapped back to > the original individual Sequences? > > A final output of the alignment in clustal (.aln) format with original > coordinates and chromosome name would be great. > > Any idea how I can solve the problem? > > > > with best regards, > > Martin > > -- > Dr. Martin Münsterkötter > MIPS - Institute of Bioinformatics and Systems Biology > Helmholtz Zentrum München > German Research Center for Environmental Health (GmbH) > Ingolstädter Landstr. 1 > 85764 Neuherberg > Germany > > http://www.helmholtz-muenchen.de/mips > > Phone: +49-89-3187-3579 > Fax: +49-89-3187-3585 > > > ________________________________________ > Von: Guy Plunkett III [[email protected]] > Gesendet: Freitag, 7. September 2012 17:59 > An: [email protected] > Betreff: Re: [Mauve-users] problem with input files in mauve > > I'm replying to Alina offlist, but I thought I'd pass on some more general > information to all. > > (1) One issue she was having resulted from FASTA files that did not have the > sequence wrapped, i.e., each sequence in the file consisted of an identifier > line and a single sequence line, regardless of sequence length. While this is > technically a valid FASTA file, Mauve doesn't deal well with them. I don't > know what line length is the maximum Mauve can deal with, and I usually wrap > sequences at something in the 60 - 80 residue range. Doing that with a file > Alina sent me did the trick. > > So how can this be accomplished? Some folks will be proficient enough that > they will just do it via command line text manipulation (regex, grep, sed, > awk, etc.). Some folks will have a favorite text editor that readily allows > such manipulations (BBEdit on Mac, for example). But the simplest solution > for many folks will be a web service running Don Gilbert's venerable Readseq. > Two such servers are <http://www.ebi.ac.uk/cgi-bin/readseq.cgi> and > <http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi>. > > Just upload your file with the Choose File button, select Pearson|Fasta|fa as > the output format under Options, and click on Submit. A file called > "readseq.cgi" is downloaded to your computer. The file is wrapped at 60 > residues/line, and works with Mauve as is (although you might want to rename > it). > > (2) The second issue was a draft genome in many contigs, where she received > the data as a directory full of individual files. For Mauve to deal with > those sequences as a single genome, you need to convert the mutiple > single-sequence files to a single multiple-sequence file. The only way I know > to do this is via command line, but it is straightforward,, and will work for > both FASTA and GenBank formats. Assuming you have all the .gbk sequences for > a genome in the directory "genome", launch the Terminal (Mac) or Command > Shell (Windows) and navigate to the directory that the "genome" directory is > in. Then type the command to merge all the files in the genome directory into > a single new file called all.gbk (or what ever name you want to use; works > for any file extension). > > On a Mac, type > cat genomes/*.gbk > all.gbk > > On Windows, type > copy /a genomes\*.gbk all.gbk > (the /a is required to ensure that the resulting file is plain text) > > Hope folks find this useful. > > Cheers, > Guy > > Dr. Guy Plunkett III > Senior Scientist, Genome Center of Wisconsin > Senior Scientist, DNASTAR > <http://www.genome.wisc.edu/information/gplunkett.html>http://www.genome.wisc.edu/information/gplunkett.html > > > ------------------------------------------------------------------------------ > 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 > > Helmholtz Zentrum München > Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) > Ingolstädter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de > Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe > Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum > Registergericht: Amtsgericht München HRB 6466 > USt-IdNr: DE 129521671 > > ------------------------------------------------------------------------------ > 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
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