Questions tagged [mauve]

Questions regarding the Multiple Genome Alignment software Mauve developed by the Darling lab.

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1 answer
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Extracting Sequence Unique to a Certain Genome

I have two genomes with high similarity. But I found out that one genome has a longer sequence of about 200 kbp. I try to align the sequence with Mauve. How can I extract this unique 200 kbp?
  • 121
6 votes
1 answer
107 views

What does it mean if aligned genomes are not of the same length?

I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used: ...
0 votes
1 answer
197 views

Find a map/correspondence between two versions of a genome

I am working with two versions of the C. elegans genome. I am finding interesting regions (specifically, tRNA genes) in version 1 and then I would like to know if version 2 also has a tRNA gene in ...
7 votes
3 answers
2k views

visualisation of genome alignment

I was asked to check the synteny of some genes in two genome assemblies of the same species (PacBio & Illumina). I was given two scaffolds couples (so 4 scaffolds total) in the Illumina genome and ...
  • 2,656
2 votes
1 answer
455 views

Can I export the SNPs between whole genome alignments using the command line?

I am using Mauve to align two whole genomes. I use the following command to get the alignment in xmfa format: ...