Body: <p>Goal: Identify conserved and variable regions within a single specific gene of interest across various species in the NCBI database.</p>
  <p>Complication: regions identified should be fixed across the single bacterial species of interest but also unique to that species of interest.</p>
  <p>Assistance needed: Identify a standard pipeline or approach that can solve the task, ideally, in a command line Linux/Unix, R, or python environment. However, Conda and Docker implementations are available tools, and windows environments can also be accessed.</p>
  <p>Further details and longform description</p>
  <p>Good afternoon,
  I have been working on a problem for a while now and think I could use some outside guidance.</p>
  <p>I would like to analyze genetic regions within a single gene across a bacterial species, and identify conserved (fixed) and variable regions, and then compare this same gene across multiple species.</p>
  <p>The species of interest is a known pathogen and I would like to identify fixed regions that the pathogen has within a specific gene of interest that are unique to a bacterial pathogen and not present in other organisms in the microenvironment.</p>
  <p>If it helps, the ideal goal would be to consider the application of RNAi as the end goal. We would like to inhibit a specific pathogen by targeting a specific well understood gene, but ideally limit the effects on the other members of the microbiome. Which is why we need to identify within the single gene of interest a region fixed across the pathogen (or at least the most prevalent strains), that is also unique specifically to the pathogen (or at least doesn't also target common members of the environment).</p>
  <p>This felt at first to be a standard problem that should have some already completed pipelines to accomplish this type of task so I was surprised to be stumped and I haven't found a standard pipeline or widely used approach. I think I may simply be thinking about the problem in the wrong way so wanted to reach out before I attempt to reinvent the wheel or head further off course.</p>
  <p>I’ve so far approached this as an aligning problem, initially looking for a way to align multiple versions of a gene across the pathogen species, the goal is to identify regions that have remained conserved (fixed) and those that have evolved (variable). But while NCBI databases have tools to blast a single version of the gene I've been unable to find tools to comb through the output and identify conserved or variable regions. Especially as I would like to look over the whole species. There are tools to identify variation on a full genome wide scale, but the current project focus is ideally only on this specific gene of interest. And because I would ideally like to cover all available sequences of the pathogen of interest for completion's sake, approaching the problem from a whole genome approach seems impractical. We really are only interested in a single gene.</p>
  <p>I think I may be approaching this task from the wrong angle, as my background is more genome wide focused. So, I thought it best to reach out. I am functional when working with command line Linux/Unix, python, R and have implemented Conda and Docker for various projects so I should be able to implement a solution using any of those tools or environments if needed.</p>
  <p>Thanks for any help or assistance you may have. Its an interesting problem and I'm looking forward to working through it with the communities guidance.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-01T01:49:30.393Z
Comments.Text: This seems more like a project planning question than a specific bioinformatics problem. What sequencing platform are you planning to concentrate on for the NCBI data? What bioinformatics tools are you planning to use for analysis?
  
  General discussion doesn't fit well on Bioinformatics Stack Exchange. If you're at the planning stage, I recommend engaging directly with a bioinformatician to talk about your project. You could also try posting on a discussion-based forum like [reddit](https://www.reddit.com/r/bioinformatics).
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-01T13:35:14.333Z
Comments.Text: It is not clear if you already have just one gene of interest (say X) or you need to start with genomic assemblies of various strains you are working with, find a set of conserved genes in this bacterial species and then test which of these genes are absent in the genomes/proteomes of a set of other species. I guess present/absent means: the full length orthologue / best reciprocal hit.
Comments.UserDisplayName: darked89
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-01T23:44:28.090Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
Tags: <rna><bacteria><multiple-sequence-alignment><ncbi><dna>
Title: Identify conserved and variable regions within a single specific gene of interest across various species in the NCBI database
ThreadText: # Identify conserved and variable regions within a single specific gene of interest across various species in the NCBI database
  
  (Asked by: username_0 on 2024-09-30)
  
  Goal: Identify conserved and variable regions within a single specific gene of interest across various species in the NCBI database.
  
  Complication: regions identified should be fixed across the single bacterial species of interest but also unique to that species of interest.
  
  Assistance needed: Identify a standard pipeline or approach that can solve the task, ideally, in a command line Linux/Unix, R, or python environment. However, Conda and Docker implementations are available tools, and windows environments can also be accessed.
  
  Further details and longform description
  
  Good afternoon,
  I have been working on a problem for a while now and think I could use some outside guidance.
  
  I would like to analyze genetic regions within a single gene across a bacterial species, and identify conserved (fixed) and variable regions, and then compare this same gene across multiple species.
  
  The species of interest is a known pathogen and I would like to identify fixed regions that the pathogen has within a specific gene of interest that are unique to a bacterial pathogen and not present in other organisms in the microenvironment.
  
  If it helps, the ideal goal would be to consider the application of RNAi as the end goal. We would like to inhibit a specific pathogen by targeting a specific well understood gene, but ideally limit the effects on the other members of the microbiome. Which is why we need to identify within the single gene of interest a region fixed across the pathogen (or at least the most prevalent strains), that is also unique specifically to the pathogen (or at least doesn't also target common members of the environment).
  
  This felt at first to be a standard problem that should have some already completed pipelines to accomplish this type of task so I was surprised to be stumped and I haven't found a standard pipeline or widely used approach. I think I may simply be thinking about the problem in the wrong way so wanted to reach out before I attempt to reinvent the wheel or head further off course.
  
  I’ve so far approached this as an aligning problem, initially looking for a way to align multiple versions of a gene across the pathogen species, the goal is to identify regions that have remained conserved (fixed) and those that have evolved (variable). But while NCBI databases have tools to blast a single version of the gene I've been unable to find tools to comb through the output and identify conserved or variable regions. Especially as I would like to look over the whole species. There are tools to identify variation on a full genome wide scale, but the current project focus is ideally only on this specific gene of interest. And because I would ideally like to cover all available sequences of the pathogen of interest for completion's sake, approaching the problem from a whole genome approach seems impractical. We really are only interested in a single gene.
  
  I think I may be approaching this task from the wrong angle, as my background is more genome wide focused. So, I thought it best to reach out. I am functional when working with command line Linux/Unix, python, R and have implemented Conda and Docker for various projects so I should be able to implement a solution using any of those tools or environments if needed.
  
  Thanks for any help or assistance you may have. Its an interesting problem and I'm looking forward to working through it with the communities guidance.
  
  **Tags:** rna, bacteria, multiple-sequence-alignment, ncbi, dna
  
  > **Comments:**
  > **username_1**: This seems more like a project planning question than a specific bioinformatics problem. What sequencing platform are you planning to concentrate on for the NCBI data? What bioinformatics tools are you planning to use for analysis?  General discussion doesn't fit well on Bioinformatics Stack Exchange. If you're at the planning stage, I recommend engaging directly with a bioinformatician to talk about your project. You could also try posting on a discussion-based forum like [reddit](https://www.reddit.com/r/bioinformatics).  
  > **username_2**: It is not clear if you already have just one gene of interest (say X) or you need to start with genomic assemblies of various strains you are working with, find a set of conserved genes in this bacterial species and then test which of these genes are absent in the genomes/proteomes of a set of other species. I guess present/absent means: the full length orthologue / best reciprocal hit.  
  > **username_3**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  
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  ## 0 answers
  
  