NCBI GeneID vs ProteinID database

Question

[biolab]

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!

[cdsouthan]

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?

[biolab]

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_... and YP_... Could you and others beifly explain to me the abbreviations (NP_, XP_, YP_, XM)? THANKS!!

Answer 1

[rwn]

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.

[biolab]

Your comments are really helpful. Thanks a lot!

Answer 2

[5heikki]

accession numbers and molecule types