Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals.Copy number variation is a type of structural variation: specifically, it is a type of duplication or deletion event that affects a considerable number of base pairs. I have a set of protein coding genes and I would like to verify them to be the product of CNV. My first idea was to overlap their domains, that are well separated by homopeptide regions but before to do this I would like to know whether more suitable indexes exist to infer this characteristic. Can anyone help?
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$\begingroup$ This is going to be rather difficult to measure, I think, with this kind of data. Where did the data come from? Would it be ok to simply find pairs of genes that are homologous? What do you mean by "product of CNV"? How would a gene be the result of a deletion? Can you give us a specific example of the kind of even that you would like to detect? $\endgroup$– Maximilian PressOct 25, 2020 at 22:22
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$\begingroup$ The data come from NCBI GenBank. Check for homologous genes and to compare their length could be a good strategy $\endgroup$– Spartan 117Oct 26, 2020 at 10:22
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2$\begingroup$ Do you mean you want to find out if a gene is a result of a gene duplication event in a species' lineage? If yes, then something like OrthoFinder could help. Usually I read CNV in reference to variation within a population genetics study. Please expand your description a bit and clarify what it is you are trying to do with more detail. $\endgroup$– Bastian SchiffthalerOct 26, 2020 at 10:41
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$\begingroup$ I have a set of genes taken from cryptosporidium parvum that show off Low Complexity regions. I would like to have a comparison with orthologs proteins and to see if they are longer than, regardless of the LCRs, orthologs. I would like to establish a connection between CNV and replication slippage if there is one. $\endgroup$– Spartan 117Oct 27, 2020 at 14:47
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