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 that region. For this, I need to know the correspondence between coordinates in genome 1 and coordinates in genome 2. I think a whole-genome alignment programme might help me, e. g. nucmer or mauve. I have run nucmer on the two genomes and got a delta file but I don't know how to interpret it. I have run show-coords on the delta file and obtained a .coords file. It seems more human-friendly. The first few lines look like this:

/Users/user/Documents/project/output/genome/celegans/ref/wormbase/seq/c_elegans.PRJNA13758.WS245.genomic.fa /Users/user/Documents/project/output/genome/celegans/strain/seq/bristol/scaffolds.fa
NUCMER

    [S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  |  [LEN R]  [LEN Q]  |  [COV R]  [COV Q]  | [TAGS]
===============================================================================================================================
       1      432  |      498      929  |      432      432  |   100.00  | 15072434 15371751  |     0.00     0.00  | I  I
       1      432  |     1002     1433  |      432      432  |   100.00  | 15072434 15371751  |     0.00     0.00  | I  I


Does this mean that chromosome I starting at 1 and ending at 432 of version 1 corresponds to chromosome I starting at 498 and ending at 929 and that there is 100% identity between these two 432-long sequences? In this case, it's easy to find a correspondence between bases in version 1 and bases in version 2. However, some lines do not align sequences of the same length:

   1   237139  |     4022   241181  |   237139   237160  |    99.99  | 15072434 15371751  |     1.57     1.54  | I  I


Also, in this sequence position 1 of chromosome I is aligned again? So is it aligning to more than one position in version 2 of the genome? Also one sequence is 237139 bases long and the other 237160 bases long. How do I know the internal structure?

Can anybody guide me, please?

I've also aligned the two genomes using Mauve:

progressiveMauve c_elegans.PRJNA13758.WS245.genomic.fa scaffolds.fa --output scaffolds.mauve &gt; scaffolds.txt


I've tried to import the .mauve file into Python using Biopython but I got an error:

alignment = SeqIO.read('scaffolds.mauve', "mauve")

Traceback (most recent call last):
  File "code/mauve.py", line 4, in &lt;module&gt;
    alignment = SeqIO.read('scaffolds.mauve', "mauve")
  File "/Users/user/anaconda/lib/python3.6/site-packages/Bio/SeqIO/__init__.py", line 712, in read
    raise ValueError("More than one record found in handle")
ValueError: More than one record found in handle


Note that the alignment opened in the Mauve GUI looks fine. Unfortunately, the picture won't load here.

I am working on Mac OSX.

I would appreciate your help in understanding the delta file, resolving the Python error or any other support in finding a function between coordinates in version 1 of the genome and coordinates in version 2 of the genome.
A relatively convenient method would be to create a .chain file, as used by tools like liftOver and crossmap (and probably remap from NCBI). For your use-case, you can simply use the DoSameSpeciesLiftOver.pl command as described in the link. The resulting chain files are pretty self-explanatory and can be used to map BED files of regions of interest.