After having run promer successfully with two genomes of different species, I'm trying to use it to map exons (as cDNA coding sequence) of 1-to-1 orthologues obtained from one of the species (which has a beautiful genome) to the other species (draft genome) to try to improve understanding of synteny.
However, it doesn't seem to be working and I would love some advice.
Essentially I have a fasta file of the CDS in nucleotides of the 1-to-1 genes - about 5000 of them - as the query.
And a fasta file of the draft genome as the reference
When I run promer, followed by show_coords I get back 128 hits.
I've tried altering l from 6 aa to just 4 aa, and increasing g from 30 aa to 1000 aa to allow for long introns etc. I'm now running it with g set at 10k aa, but I don't think it's going to make a difference because I've looked at one of the genes that does have hits and I don't think that long introns are the issue.
I'm trying to figure out just what a cluster is - if I just have a hit, but it's not clustered with another hit does it get dropped from the output?
Here is my current promer code:
promer -l 4 -g 10000 ref.fasta one2one_cds.fa
And my show_coords code:
show-coords -k -l -T -q out.delta > one2one.coords
Hi,
After having run promer successfully with two genomes of different species, I'm trying to use it to map exons (as cDNA coding sequence) of 1-to-1 orthologues obtained from one of the species (which has a beautiful genome) to the other species (draft genome) to try to improve understanding of synteny.
However, it doesn't seem to be working and I would love some advice.
Essentially I have a fasta file of the CDS in nucleotides of the 1-to-1 genes - about 5000 of them - as the query. And a fasta file of the draft genome as the reference
When I run promer, followed by show_coords I get back 128 hits. I've tried altering l from 6 aa to just 4 aa, and increasing g from 30 aa to 1000 aa to allow for long introns etc. I'm now running it with g set at 10k aa, but I don't think it's going to make a difference because I've looked at one of the genes that does have hits and I don't think that long introns are the issue.
I'm trying to figure out just what a cluster is - if I just have a hit, but it's not clustered with another hit does it get dropped from the output?
Here is my current promer code:
promer -l 4 -g 10000 ref.fasta one2one_cds.faAnd my show_coords code:
show-coords -k -l -T -q out.delta > one2one.coordsAny help would be much appreciated! Thanks, Jenni