Answers.Body: <p>Yes, UniProt is the most comprehensive database of protein sequences we have. Or, at any rate, the most comprehensive one I know. However, if you're looking for neuraminidases, don't try and find them using blast. While blast can indeed be part of a pipeline designed to find homologous sequences, it isn't enough by itself and just running blast to get similar sequences is not a good way of finding actual homologs if you don't know what you're doing, apply correct filters etc.</p>
  <p>Instead, if you have your species of interest, you can look up the proteins in UniProt or simply NCBI's RefSeq databases. You also have various databases that host collections of homologous sequences. Don't reinvent the wheel. You might want to post a new question, explaining exactly what kind of sequences you need and asking for help on obtaining them. But really, don't try and just blast your way to a set of homologs, that is quite a complicated job to get right.</p>
  
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Body: <p>I am going to study neuraminidase and hemaglutinin, proteins of interest for influenza virus vaccines. My first step is going to be to find all the protein sequences I can, make databases of my own in order to study them. I started using uniprot mostly and looking for similar proteins with BLAST. My main question is actually a string of related questions that I am going to leave here:</p>
  <p>Does Uniprot have all the proteins that are known? If not, is there such a database? If not, do I combine results from multiple databases? What would other good databases like Uniprot be?</p>
  <p>I have other questions like: How do i make sure i dont leave out some proteins? Is it worth thinking about this or is it inevitable? etc. but I dont think asking everything here would be efficient.</p>
  <p>Thank you for your time! (And sorry for any dumb question)</p>
  <p>EDIT(context): I am looking for neuraminidase sequences from influenza, the final purpose is to find epitopes and the corresponding antibody structures to interact with those epitopes. As for the specific analyses that I will do, I am in a very early stage and I am not sure of that myself as I am still learning. As for blast, I am getting acquainted with it now, i used it to find similar sequences to the ones I selected, though I am also unsure about what to select and how to properly use it. I am reading the documentation and trying to figure those things out at the moment but this is the general context.</p>
  
Tags: <proteins><sequence-analysis><database>
Title: What are some good protein databases to use? Trying to find neuraminidase sequences for influenza
ThreadText: # What are some good protein databases to use? Trying to find neuraminidase sequences for influenza
  
  (Asked by: username_0 on 2024-10-17)
  
  I am going to study neuraminidase and hemaglutinin, proteins of interest for influenza virus vaccines. My first step is going to be to find all the protein sequences I can, make databases of my own in order to study them. I started using uniprot mostly and looking for similar proteins with BLAST. My main question is actually a string of related questions that I am going to leave here:
  
  Does Uniprot have all the proteins that are known? If not, is there such a database? If not, do I combine results from multiple databases? What would other good databases like Uniprot be?
  
  I have other questions like: How do i make sure i dont leave out some proteins? Is it worth thinking about this or is it inevitable? etc. but I dont think asking everything here would be efficient.
  
  Thank you for your time! (And sorry for any dumb question)
  
  EDIT(context): I am looking for neuraminidase sequences from influenza, the final purpose is to find epitopes and the corresponding antibody structures to interact with those epitopes. As for the specific analyses that I will do, I am in a very early stage and I am not sure of that myself as I am still learning. As for blast, I am getting acquainted with it now, i used it to find similar sequences to the ones I selected, though I am also unsure about what to select and how to properly use it. I am reading the documentation and trying to figure those things out at the moment but this is the general context.
  
  **Tags:** proteins, sequence-analysis, database
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2024-10-17. Score: 1 | Accepted answer
  
  Yes, UniProt is the most comprehensive database of protein sequences we have. Or, at any rate, the most comprehensive one I know. However, if you're looking for neuraminidases, don't try and find them using blast. While blast can indeed be part of a pipeline designed to find homologous sequences, it isn't enough by itself and just running blast to get similar sequences is not a good way of finding actual homologs if you don't know what you're doing, apply correct filters etc.
  
  Instead, if you have your species of interest, you can look up the proteins in UniProt or simply NCBI's RefSeq databases. You also have various databases that host collections of homologous sequences. Don't reinvent the wheel. You might want to post a new question, explaining exactly what kind of sequences you need and asking for help on obtaining them. But really, don't try and just blast your way to a set of homologs, that is quite a complicated job to get right.
  
  
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