Can liftover utilities of UCSE browser be used for bacterial genomic coordinates?

Question

[sharmatina189059]

I have coordinates of different version of same bacterial genome. I want to compare coordinates obtained from both genomes. Can the liftover utilities be used for this purpose. if yes, how can I use this.

I have file like this for both the genomes.

chr1    start     end                                 chr1     start     end

Answer 1

[genecats.ucsc]

Liftover will work just fine for bacterial sequences as long as you have created the liftover chain files for the alignment between the two genomes. Making these liftover chains is not trivial, but here is some information on the process: http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto

If you have questions, feel free to send them to one of our mailing lists:

• [e-mail] for general questions (public list)
• [e-mail] for question concerning private data (private list)
• [e-mail] for questions concerning the setup and running of your own UCSC Genome Browser installation

ChrisL from the UCSC Genome Browser