Questions tagged [mauve]

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

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How to reverse complement a genbank file?

I am visualizing the alignment of a particular genomic region across different genomes with mauve. In certain genomes the region of interest is in the negative strand and in others the positive strand....
venkatesh war's user avatar
0 votes
0 answers
26 views

Error while opening xmfa generated by progressiveMauve

I used commandline progressiveMauve to align two genome .gbk files. The alignment was successful. But when I try to visualize the final .xmfa file with Mauve, I get the following error. ...
venkatesh war's user avatar
2 votes
0 answers
157 views

Drawing synteny using CIRCOS from progressive MAUVE alignment

I am using Mauve app to align two whole genomes. I've aligned these genomes (gbk files) with the progressive Mauve aligner, and I got sp.sslist, sp.xmfa, sp.guide_tree,sp.backbone file, sp.bbcols etc ...
Umar's user avatar
  • 135
0 votes
1 answer
97 views

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?
raysteven's user avatar
7 votes
1 answer
164 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: ...
Anthony Guterres's user avatar
0 votes
1 answer
315 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 ...
Biomagician's user avatar
  • 2,459
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 ...
aechchiki's user avatar
  • 2,676
2 votes
1 answer
536 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: ...
Biomagician's user avatar
  • 2,459