extract annotation for mVISTA whole genome comparison

Question

[slimane.khayi]

Dear all, I need to perform whole genome comparisons within cp genomes and I have to prepare specific annotation files to feed mVISTA server as described below :

< 106481 116661 gene1 
106481 106497 utr 
107983 108069 exon 
109884 110033 exon 
111865 112023 exon 

> 39424 42368 gene2 
39424 39820 exon 
41401 42368 exon

> 77817 81088 gene3
77817 78820 utr 
79538 80107 exon

Do you have any tool that could help me to extract automatically these information from gbk files. Thank you in advance.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Answer 1

[Michael G]

I have written a blog post about how to set up a custom annotation file for the visualization of several genomes via mVISTA. The post includes an example using the plastid genome of Arabidopsis thaliana (i.e., is accessible to everyone via NCBI GenBank).

You can find that post here: https://blogs.fu-berlin.de/gruenstaeudl/2020/10/12/buena-vista-con-mvista/