<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>

CC BY-SA 4.0
2024-10-22T02:22:40.580Z
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?
gringer
CC BY-SA 4.0
2024-10-22T02:23:34.963Z
What will you do with these IDs after the conversion? What downstream program(s) do you want to use?
gringer
CC BY-SA 4.0
2024-10-22T19:09:14.603Z
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?
terdon
CC BY-SA 4.0
2024-10-23T02:35:28.337Z
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.
Community
<r><proteins><kegg><refseq>
Help converting NCBI RefSeq list to Other Database
# 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

