Body: <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-25T22:22:49.467Z
Comments.Text: 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?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-26T10:22:13.627Z
Comments.Text: The data come from NCBI GenBank. Check for homologous genes and to compare their length could be a good strategy
Comments.UserDisplayName: Spartan 117
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-26T10:41:24.557Z
Comments.Text: 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](https://davidemms.github.io/) 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.
Comments.UserDisplayName: Bastian Schiffthaler
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-27T14:47:09.860Z
Comments.Text: 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.
Comments.UserDisplayName: Spartan 117
Tags: <protein-structure><genetics><copy-number>
Title: How to see if a gene is the product of copy number variation?
ThreadText: # How to see if a gene is the product of copy number variation?
  
  (Asked by: username_0 on 2020-10-24)
  
  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?
  
  **Tags:** protein-structure, genetics, copy-number
  
  > **Comments:**
  > **username_1**: 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?  
  > **username_0**: The data come from NCBI GenBank. Check for homologous genes and to compare their length could be a good strategy  
  > **username_2**: 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](https://davidemms.github.io/) 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.  
  > **username_0**: 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.  
  
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  ## 0 answers
  
  