Hi! Thank you for providing this great tool.
I am comparing several accessions of the same species and I am observing surprisingly low gene collinearity values: with the default parameters, I never obtain more than 50% collinearity between accessions, which seems unexpectedly low for intra-species comparisons.
To investigate this further, I even ran MCScanX on one accession against itself, expecting to recover close to 100% of genes as collinear, but instead I obtained an extremely low value of 0.16. I tried adjusting many parameters (including gap sizes, match thresholds, etc.) and also increased the number of allowed BLASTP hits per gene, but none of these changes improved the situation ; in fact, increasing the number of BLAST hits surprisingly made the collinearity score drop even further. I also manually checked BLAST results and confirmed that strong, consistent hits exist, yet they do not appear in the final collinearity output.
Has anyone encountered this type of issue before, and do you have suggestions for understanding why collinearity values remain so low, even for a self–self comparison? Any help would be greatly appreciated!
Ncci_against_itself.blast.gz
Ncci_against_itself.collinearity.gz
Ncci_against_itself.gff.gz
Ncci_against_itself.tandem.gz
Hi! Thank you for providing this great tool.
I am comparing several accessions of the same species and I am observing surprisingly low gene collinearity values: with the default parameters, I never obtain more than 50% collinearity between accessions, which seems unexpectedly low for intra-species comparisons.
To investigate this further, I even ran MCScanX on one accession against itself, expecting to recover close to 100% of genes as collinear, but instead I obtained an extremely low value of 0.16. I tried adjusting many parameters (including gap sizes, match thresholds, etc.) and also increased the number of allowed BLASTP hits per gene, but none of these changes improved the situation ; in fact, increasing the number of BLAST hits surprisingly made the collinearity score drop even further. I also manually checked BLAST results and confirmed that strong, consistent hits exist, yet they do not appear in the final collinearity output.
Has anyone encountered this type of issue before, and do you have suggestions for understanding why collinearity values remain so low, even for a self–self comparison? Any help would be greatly appreciated!
Ncci_against_itself.blast.gz
Ncci_against_itself.collinearity.gz
Ncci_against_itself.gff.gz
Ncci_against_itself.tandem.gz