Hi Mark,
Thank for your suggestion. I tried different genome sequences and
discovered that .fna and .gbk files work perfectly. However, I still have
problems with my genome sequences, which are in different file format. At
least I know that Mauve installed correctly on my PC :)
Cheers,
Alina
On Thu, Sep 6, 2012 at 9:12 AM, Been-2, M.W.H. de <[email protected]>wrote:
> Hi Alina,
> I have used Mauve a few times and at least with *.fna files under
> ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ it always worked (BTW:
> right-click on fna-file and save-link-as in windows should work to download
> the file). Perhaps you can try 2 small sequences first to see if your Mauve
> installation is actually correct.
> cheers
> Mark
>
> --
> Mark de Been, PhD
> Department of Medical Microbiology
> University Medical Center Utrecht (UMCU)
> Heidelberglaan 100; Room G04.613
> 3584 CX Utrecht
> The Netherlands
> e-mail: [email protected]
> tel. +31-887557627
> fax +31-302541770
> --
>
> ________________________________
> From: Alina Grigorescu [[email protected]]
> Sent: 05 September 2012 16:35
> To: [email protected]
> Subject: [Mauve-users] problem with input files in mauve
>
> 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
> [email protected]<mailto:[email protected]>
> [email protected]<mailto:[email protected]>
>
> Postodctoral Researcher
> Centre Wallon de Biologie Industrielle
> Universite de Liege
> Sart-Tilman, B40
> Tel: +3243663997
>
>
>
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--
Alina Grigorescu, PhD
[email protected]
[email protected]
Postodctoral Researcher
Centre Wallon de Biologie Industrielle
Universite de Liege
Sart-Tilman, B40
Tel: +3243663997
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