Answers.Body: <p>Prokka is an easy-to-use pipeline for the annotation of bacterial genomes. Here is the link to the GitHub page: <a href="https://github.com/tseemann/prokka" rel="nofollow noreferrer">https://github.com/tseemann/prokka</a></p>
  <p>nic</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-11-05T16:25:36.043Z
Answers.LastActivityDate: 2024-11-05T16:25:36.043Z
Answers.UserDisplayName: nicolotellini
Answers.Body: <p>What is the dataset you are working from? Are you working from finished, annotated genomes, raw sequencing data, de novo assemblies, ...?</p>
  <p>The simplest answer would be to go to a genome database such as <a href="https://www.genome.jp/kegg/genome/" rel="nofollow noreferrer">KEGG</a> and look up the relevant genes. <a href="https://www.microbesonline.org/" rel="nofollow noreferrer">MicrobesOnline</a> and <a href="https://www.ncbi.nlm.nih.gov/research/cog/" rel="nofollow noreferrer">COGs</a> are other resource I've used, but there are likely newer ones.</p>
  <p>If you simply query the gene in such a database, you should get a list of entries and the relevant genomes that they're in, and you then get the copy number of the gene in the genome for free. <a href="https://www.microbesonline.org/cgi-bin/keywordSearch.cgi?type=0&amp;mapId=01100&amp;keggCid=0&amp;ec=0&amp;term=1&amp;locus=0&amp;hit=0&amp;disp=0&amp;homolog=0&amp;format=1&amp;favorites=&amp;byFavorites=1&amp;taxId=511145&amp;taxId=224308&amp;taxId=882&amp;taxId=391774&amp;taxId=264203&amp;taxId=211586&amp;taxId=207559&amp;taxId=269799&amp;taxId=243231&amp;taxId=264462&amp;taxId=177439&amp;taxId=477974&amp;keyword=hsp90" rel="nofollow noreferrer">Here</a> is such a page on MicrobesOnline.</p>
  <p>The one caution that I have is to really understand the orthology of the gene you're interested in.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-12-05T18:41:37.910Z
Answers.LastActivityDate: 2024-12-05T18:41:37.910Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I would like to know if there is an easy tool to find how many copies of a certain gene are present in all available bacterial genomes.</p>
  <p>For example, which bacterial genomes contain one or more copies of Superoxide dismutase.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-30T15:11:57.300Z
Comments.Text: Simply use RNAseq tools such as EdgeR, each gene must be a separate entity, e.g. separate fasta entry for this approach. This is one approach, there are lots. Probably a good idea to provide more details.
Comments.UserDisplayName: M__
Tags: <gene><bacteria><duplications>
Title: Finding gene duplications in bacteria
ThreadText: # Finding gene duplications in bacteria
  
  (Asked by: username_0 on 2024-10-30)
  
  I would like to know if there is an easy tool to find how many copies of a certain gene are present in all available bacterial genomes.
  
  For example, which bacterial genomes contain one or more copies of Superoxide dismutase.
  
  **Tags:** gene, bacteria, duplications
  
  > **Comments:**
  > **username_1**: Simply use RNAseq tools such as EdgeR, each gene must be a separate entity, e.g. separate fasta entry for this approach. This is one approach, there are lots. Probably a good idea to provide more details.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2024-11-05. Score: 0
  
  Prokka is an easy-to-use pipeline for the annotation of bacterial genomes. Here is the link to the GitHub page: <https://github.com/tseemann/prokka>
  
  nic
  
  
  ---
  
  ### Answer by username_3 on 2024-12-05. Score: 0
  
  What is the dataset you are working from? Are you working from finished, annotated genomes, raw sequencing data, de novo assemblies, ...?
  
  The simplest answer would be to go to a genome database such as [KEGG](https://www.genome.jp/kegg/genome/) and look up the relevant genes. [MicrobesOnline](https://www.microbesonline.org/) and [COGs](https://www.ncbi.nlm.nih.gov/research/cog/) are other resource I've used, but there are likely newer ones.
  
  If you simply query the gene in such a database, you should get a list of entries and the relevant genomes that they're in, and you then get the copy number of the gene in the genome for free. [Here](https://www.microbesonline.org/cgi-bin/keywordSearch.cgi?type=0&mapId=01100&keggCid=0&ec=0&term=1&locus=0&hit=0&disp=0&homolog=0&format=1&favorites=&byFavorites=1&taxId=511145&taxId=224308&taxId=882&taxId=391774&taxId=264203&taxId=211586&taxId=207559&taxId=269799&taxId=243231&taxId=264462&taxId=177439&taxId=477974&keyword=hsp90) is such a page on MicrobesOnline.
  
  The one caution that I have is to really understand the orthology of the gene you're interested in.
  
  
  ---
  
  