Body: <p>I've got gene sequences of mouse genes. Each sequence contains variants from the reference genome. I need to find out whether these SNPs/variations are in functionally significant regions (i.e. exons).</p>
  <p>I also need to see if these SNPs/mutations are conserved across species.</p>
  <p>I'm not very proficient in this, but would BLAST or ENSEMBL be useful here? Is there an easy way to search this? I have the sequences as .txt files. I'm proficient in Python if that's useful as well.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-27T06:35:30.510Z
Comments.Text: search for variant annotation tools. I can think of VEP in Ensembl, SnpEff, .. You would need your variants in VCF format (possibly other formats) and the tools annotate each variant with various qualitative/quantitative metrics you require
Comments.UserDisplayName: JRodrigoF
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-27T09:44:54.357Z
Comments.Text: VEP online: https://www.ensembl.org/Tools/VEP
Comments.UserDisplayName: Matteo Ferla
Tags: <blast><ensembl>
Title: Identifying Variant Conservation Across Species
ThreadText: # Identifying Variant Conservation Across Species
  
  (Asked by: username_0 on 2021-10-26)
  
  I've got gene sequences of mouse genes. Each sequence contains variants from the reference genome. I need to find out whether these SNPs/variations are in functionally significant regions (i.e. exons).
  
  I also need to see if these SNPs/mutations are conserved across species.
  
  I'm not very proficient in this, but would BLAST or ENSEMBL be useful here? Is there an easy way to search this? I have the sequences as .txt files. I'm proficient in Python if that's useful as well.
  
  **Tags:** blast, ensembl
  
  > **Comments:**
  > **username_1**: search for variant annotation tools. I can think of VEP in Ensembl, SnpEff, .. You would need your variants in VCF format (possibly other formats) and the tools annotate each variant with various qualitative/quantitative metrics you require  
  > **username_2**: VEP online: https://www.ensembl.org/Tools/VEP  
  
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  ## 0 answers
  
  