How to extract BED-format annotation tracks for the newly inserted segments

I used the Mauve software package to compute a multiple genome alignment across a dozen Agrobacterium genomes. How can I use the Mauve output to generate BED-format annotation tracks for newly inserted segments?

bed mauve

• 532 views • link

updated 2.4 years ago by Ram

• written 2.4 years ago by FZ •

0 answers

No answers yet.

More posts like this

How to visualize multiple bacterial genomes with circos?
written 2.5 years ago by marongiu.luigi

I am trying to use [circos][1] to visualize the alignment of multiple bacterial genomes (essentially to create a genome atlas like this: ![enter image description …
Extraction of LCBs in MAUVE programme
written 5.8 years ago by amresharma1 •

I did multiple genomes alignment in Mauve programme. Now I wish to extract LCBs which are orthologous in each genome. Please suggest me how do …
Mauve Alignment Viewer
written 6.4 years ago by biohacker_tobe •

Hello community, I was able to conduct a multiple whole genome alignment of my strains with ProgressiveMauve, however I want to visualize my alignment possible …
Gene Cluster Annotation
written 6.4 years ago by biohacker_tobe •

Hey community :) I want to first conduct an alignment on my bacterial genomes (these vary in size) for which I was thinking of using …
Region of differences using Mauve
written 7.7 years ago by shweta.alai236 •

I want to find region of difference (RDs) in my bacterial genomes. I came across on literature suggesting that Mauve output was used to extract …
Adding annotation tracks for multiple alignment
written 7.9 years ago by tim.ivanov.92 •

Is there a software to add annotation to multiple alignments? I have a file from clustalw/muscle with multiple alignment of DNA regions. And i want …
LDheatmap with custom genome
written 9.8 years ago by tkarasov •

Hi, I am working with 1001 genomes data for A. thaliana, attempting to look at Linkage Disequilibrium throughout the genome. Using a combination of plink …
Genome annotation by RAST
written 11.5 years ago by norhanmahfouz •

Hi, I have used RAST command line tools, namely `find_rnas`, `call_genes` and `svr_assign_using_figfams` for the annotation of my 50+ set of ordered contigs; the output …
How to generate identity matrix files using Mauve?
written 11.8 years ago by nkuyfq

<p>I am using Mauve to compare multiple genomes. On the mannual page http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html, the author said an identity matrix file of the genomes compared could …
Genbank to bed conversion for bedtools analysis
written 12.0 years ago by susan.klein •

Hi, I need to use bedtools to obtain the coverage across two bam files for comparison. However, to do this, I need a .bed file …