Body: <p>I am writing a project proposal for my boss and it is on codon usage bias in the dystrophin protein and the spectrin-like repeats found in a hmmscan file using the longest dystrophin isoform protein sequence which I got from a GenBank file!</p>
  <p>There is a lot of research on how mRNA and tRNA impact codon usage bias and codon frequency.  Long story short, I work at a gene therapy lab as a bioinformatician doing research for muscular dystrophy.  Our lab is very interested in miRNA, and I have found a certain amount of articles that show miRNA may impact codon usage bias since miRNA can either cleave or translationally repress mRNA.</p>
  <p>I found a miRNA database called <a href="http://www.tools4mirs.org" rel="nofollow noreferrer">www.tools4mirs.org</a>. It seems like a potentially good database, but I don't know if it's the right database geared for this project.  We saw some unusual lack of protein expression when there should be a lot of protein expression and our lab is really focused on an interested in miRNAs.</p>
  <p>Are there any other miRNA databases/tools that you can recommend?</p>
  <p>I code in Python and know some AI/ML and would like to make this project a AI/ML bioinformatics project, but I do not know what some good miRNA databases are, since I want to pull large amounts of miRNA data for my project that is relative to muscular dystrophy.</p>
  <p>So to sum up my question, what are some really heavily and well-curated miRNA databases besides tools4mirs.org ? I am kind of new to this field, and would like to hear any suggestion since I am still learning the inner workings of the field of bioinformatics and the possibilities and directions it can go in.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-04T02:00:12.483Z
Comments.Text: Welcome to the site. I would first use Ncbi's SRA. Every miRNA study will need to upload there and I'd use the sratoolkit.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-04T13:47:37.673Z
Comments.Text: Good databases for what? What kind of data do you need? Sequences? Functional annotations? Variants? Population data? What species? A specific one? Any? What does protein expression have to do with it?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-05T15:27:11.967Z
Comments.Text: miRNA databases with functional annotations and structural annotations for humans is what I am looking for.  I am looking at the concept of translation/reverse translation and miRNA regulation of mRNA which impacts tRNA/anti-codons
Comments.UserDisplayName: Rachel Sweeney
Tags: <python><proteins><genomics><rna><genetics>
Title: What are some good miRNA databases?
ThreadText: # What are some good miRNA databases?
  
  (Asked by: username_0 on 2023-11-03)
  
  I am writing a project proposal for my boss and it is on codon usage bias in the dystrophin protein and the spectrin-like repeats found in a hmmscan file using the longest dystrophin isoform protein sequence which I got from a GenBank file!
  
  There is a lot of research on how mRNA and tRNA impact codon usage bias and codon frequency. Long story short, I work at a gene therapy lab as a bioinformatician doing research for muscular dystrophy. Our lab is very interested in miRNA, and I have found a certain amount of articles that show miRNA may impact codon usage bias since miRNA can either cleave or translationally repress mRNA.
  
  I found a miRNA database called [www.tools4mirs.org](http://www.tools4mirs.org). It seems like a potentially good database, but I don't know if it's the right database geared for this project. We saw some unusual lack of protein expression when there should be a lot of protein expression and our lab is really focused on an interested in miRNAs.
  
  Are there any other miRNA databases/tools that you can recommend?
  
  I code in Python and know some AI/ML and would like to make this project a AI/ML bioinformatics project, but I do not know what some good miRNA databases are, since I want to pull large amounts of miRNA data for my project that is relative to muscular dystrophy.
  
  So to sum up my question, what are some really heavily and well-curated miRNA databases besides tools4mirs.org ? I am kind of new to this field, and would like to hear any suggestion since I am still learning the inner workings of the field of bioinformatics and the possibilities and directions it can go in.
  
  **Tags:** python, proteins, genomics, rna, genetics
  
  > **Comments:**
  > **username_1**: Welcome to the site. I would first use Ncbi's SRA. Every miRNA study will need to upload there and I'd use the sratoolkit.  
  > **username_2**: Good databases for what? What kind of data do you need? Sequences? Functional annotations? Variants? Population data? What species? A specific one? Any? What does protein expression have to do with it?  
  > **username_0**: miRNA databases with functional annotations and structural annotations for humans is what I am looking for.  I am looking at the concept of translation/reverse translation and miRNA regulation of mRNA which impacts tRNA/anti-codons  
  
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  ## 0 answers
  
  