NCBI GeneID vs ProteinID database
Hi everyone
I am looking for NCBI ProteinID vs GeneId pair database as well as Gene seq database, because I have a comprehensive list of protein IDs and need to convert them to Gene IDs, and then get corresponding sequences.
I should note I tried an online convertion tool, but run too slow because of a huge list.
I log on NCBI Gene ftp site and found a couple of dbs available for download. I am wondering if it is the correct place to download? I cannot find fasta data there.
THANKS A LOT in advance for your advice and help!
2 answers
From the NCBI website About RefSeq:
Definitions:
- Model RefSeq: RNA and protein products that are generated by the eukaryotic genome annotation pipeline. These records use accession prefixes XM_, XR_, and XP_.
- Known RefSeq: RNA and protein products that are mainly derived from GenBank cDNA and EST data and are supported by the RefSeq eukaryotic curation group. These records use accession prefixes NM_, NR_, and NP_.
Hope that helps a bit.
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This needs clarification please. Proteins and genes are different concepts. Also there are many protein ID types. What exactly do you want to map to what?
Hi cdsouthan,
Thanks a lot for your reply. I finally sorted out the problem. I found my aim databases on NCBI ftp website. Actually my protein list only includes
NP_...XP_... andYP_... Could you and others beifly explain to me the abbreviations (NP_,XP_,YP_,XM)? THANKS!!