Body: <p>I am trying to find neuraminidase sequences from influenza virus to work with (as many as possible if not ideally everything available) and I have been using NCBI Virus for this (<a href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Protein&amp;VirusLineage_ss=taxid:197911&amp;VirusLineage_ss=taxid:197912&amp;VirusLineage_ss=taxid:197913&amp;VirusLineage_ss=taxid:1511083&amp;ProtNames_ss=neuraminidase&amp;ProtNames_ss=Neuraminidase&amp;ProtNames_ss=neuraminidase%20glycoprotein&amp;ProtNames_ss=neuraminidase%20surface%20protein" rel="nofollow noreferrer">this is my search query</a>).</p>
  <p>How can I eliminate the neuraminidase sequences that are only theoretically determined? I need only protein level data, experimental evidence (i.e. &quot;Experimental evidence at protein level&quot; according to <a href="https://www.uniprot.org/help/protein_existence" rel="nofollow noreferrer">this</a>). When using uniprot to look for neuraminidase (uniprot.org/uniprotkb?query=neuraminidase) i can filter by &quot;protein existence&quot; and one of the options is &quot;protein level&quot;, but I couldn't identify a filter in NCBI Virus for this.</p>
  <p>Thank you!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-23T18:37:54.077Z
Comments.Text: Just switch to NCBI and use the online Blast if the sequences sought are less than ~50K (I forget the upper limit and I think it's been lowered). Otherwise perform a local Blast. Generally, theoretical sequences are removed from NBCI and if present will be clearly tagged.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-23T18:45:40.813Z
Comments.Text: Maybe I'm misunderstanding but the "protein level" stuff has very little relationship to the sequences themselves- it's more an annotation confidence thing. If you really restricted to that level, you might find that you have only 5-10 NA sequences total, because that's the number that have had X-ray structures solved (or whatever). Basically no one is isolating / directly detecting NA protein from their samples when they register NA sequences, because it's immensely laborious to do so. I think that the assumption is that if it's a flu virus and has an NA sequence, that's good enough.
Comments.UserDisplayName: Maximilian Press
Tags: <proteins><sequence-analysis><public-databases><virus>
Title: NCBI Virus experimentally determined proteins
ThreadText: # NCBI Virus experimentally determined proteins
  
  (Asked by: username_0 on 2024-10-20)
  
  I am trying to find neuraminidase sequences from influenza virus to work with (as many as possible if not ideally everything available) and I have been using NCBI Virus for this ([this is my search query](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Protein&VirusLineage_ss=taxid:197911&VirusLineage_ss=taxid:197912&VirusLineage_ss=taxid:197913&VirusLineage_ss=taxid:1511083&ProtNames_ss=neuraminidase&ProtNames_ss=Neuraminidase&ProtNames_ss=neuraminidase%20glycoprotein&ProtNames_ss=neuraminidase%20surface%20protein)).
  
  How can I eliminate the neuraminidase sequences that are only theoretically determined? I need only protein level data, experimental evidence (i.e. "Experimental evidence at protein level" according to [this](https://www.uniprot.org/help/protein_existence)). When using uniprot to look for neuraminidase (uniprot.org/uniprotkb?query=neuraminidase) i can filter by "protein existence" and one of the options is "protein level", but I couldn't identify a filter in NCBI Virus for this.
  
  Thank you!
  
  **Tags:** proteins, sequence-analysis, public-databases, virus
  
  > **Comments:**
  > **username_1**: Just switch to NCBI and use the online Blast if the sequences sought are less than ~50K (I forget the upper limit and I think it's been lowered). Otherwise perform a local Blast. Generally, theoretical sequences are removed from NBCI and if present will be clearly tagged.  
  > **username_2**: Maybe I'm misunderstanding but the "protein level" stuff has very little relationship to the sequences themselves- it's more an annotation confidence thing. If you really restricted to that level, you might find that you have only 5-10 NA sequences total, because that's the number that have had X-ray structures solved (or whatever). Basically no one is isolating / directly detecting NA protein from their samples when they register NA sequences, because it's immensely laborious to do so. I think that the assumption is that if it's a flu virus and has an NA sequence, that's good enough.  
  
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  ## 0 answers
  
  