Body: <p>I have a list of NCBI RefSeq numbers (with corresponding sequences) that I would like to convert/map to any of the following formats:</p>
  <p>Pfam, TIGRfams, SMART ID, SMART name, SUPERAM ID, SUPERFam Name, CATH FunFam ID, CathFunFAm Name, Enzyme, KEGG Pathway Enzymes, KEGG IDs, KEGG Names, KEGG Orthoology Defintions, MetaCyc. I am really struggling to do this through a variety of tools (HMMER, rHMMER, etc). Is there an easier way to do this? Ideally it would not be through sequence annotation because I have a very large number of sequences. I have the most experience using R if programming is the way to go.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-22T02:22:40.580Z
Comments.Text: What do you want to do with mappings that are not one-to-one, i.e. NCBI IDs with no mapping, or NCBI IDs with multiple mappings?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-22T02:23:34.963Z
Comments.Text: What will you do with these IDs after the conversion? What downstream program(s) do you want to use?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-22T19:09:14.603Z
Comments.Text: Also, please [edit] your question and give us at least one example input and the output you would want from it. Are these refSeq transcripts or proteins? Or something else? What species?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-23T02:35:28.337Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Tags: <r><proteins><kegg><refseq>
Title: Help converting NCBI RefSeq list to Other Database
ThreadText: # Help converting NCBI RefSeq list to Other Database
  
  (Asked by: username_0 on 2024-10-21)
  
  I have a list of NCBI RefSeq numbers (with corresponding sequences) that I would like to convert/map to any of the following formats:
  
  Pfam, TIGRfams, SMART ID, SMART name, SUPERAM ID, SUPERFam Name, CATH FunFam ID, CathFunFAm Name, Enzyme, KEGG Pathway Enzymes, KEGG IDs, KEGG Names, KEGG Orthoology Defintions, MetaCyc. I am really struggling to do this through a variety of tools (HMMER, rHMMER, etc). Is there an easier way to do this? Ideally it would not be through sequence annotation because I have a very large number of sequences. I have the most experience using R if programming is the way to go.
  
  **Tags:** r, proteins, kegg, refseq
  
  > **Comments:**
  > **username_1**: What do you want to do with mappings that are not one-to-one, i.e. NCBI IDs with no mapping, or NCBI IDs with multiple mappings?  
  > **username_1**: What will you do with these IDs after the conversion? What downstream program(s) do you want to use?  
  > **username_2**: Also, please [edit] your question and give us at least one example input and the output you would want from it. Are these refSeq transcripts or proteins? Or something else? What species?  
  > **username_3**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  
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  ## 0 answers
  
  