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
grigo...@umn.edu
agrigore...@ulg.ac.be
Postodctoral Researcher
Centre Wallon de Biologie Industrielle
Universite de Liege
Sart-Tilman, B40
Tel: +3243663997
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