non-monomeric regions in centromeres

[prometheusloong]

Hi, I found that the softeare could identifies non-monomeric regions in centromeres from CentromereArchitect paper. But i didn't find the "CenromereDecomposer" module. I put cento sequence and a gene sequence (in centromere region) as monomers fasta, and run monomer_inference.py. The result as same as inputing cento sequnece only. Maybe the gene sequence is not repeat or too long? Could you help me? Thanks!

[TanyaDvorkina]

Hello!

Thank you for using StringDecomposer and CentromereArchitect! Try our latest release of CentromereArchitect (now HORmon) that can be found here github.com/ablab/HORmon. HORmon uses StringDecomposer and CentromereArchitect as part of its pipeline.

I am not sure I understand what your goal is. All our tools have two main parameters 1) centromeric sequence(s) (can be reads or reference) 2) monomer sequence(s). Now we work only with human centromeres. Monomer sequence there has length around 150-200bp and it is not a gene sequence.

Non-monomeric regions can be detected by low monomers identity in such regions (can be found in file final_decomposition.tsv).

Hope it will help! Please do not hesitate to ask further questions!

Best, Tatiana