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 > 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 <module> 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.