Sibelia not detecting perfect palindrome?

Hello,

I have a simulated dataset, with a chromosome which contains a "perfect palindrome", which means the reverse complement is directly downstream to the primary sequence without intervening nucleotides.

Strangely, Sibelia, be it with -s loose or -s fine doesn't detect it. However, if I copy that palindrome sequence and ask Sibelia to search for syntheny between it and the chromosome it's copied from, then the palindrome is reported.

I can easily provide the file if needed.

Thanks a lot

[iminkin]

Do you use exactly the same parameters -m?

Yes! the parameters are the same

[iminkin]

It could be:

1. Other parts of the graph interferring with the part of the genomes you are interested in. It may hinder the bubble collapsing algorithm or something else

2. Could be a software bug

3. Something else

I have to take a closer look to be more precise.