Question: Converting Cdd Pssm Ids To Pdb Or Interpro Id
1
gravatar for ben.readhead
7.2 years ago by
ben.readhead20
ben.readhead20 wrote:

Hi everyone,

I'm hoping someone may have come across this one before. I've been using NCBIs Conserved Domain Database and have a list of PSSM IDs I'd like to map to some other ID (such as PDB or interpro) to allow me to work with some of the domain-domain interaction databases.

I've taken a look at the NCBI FTP site (ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/), and the closest I've come is the cdd.versions file which allows mapping between a CD accession number, a 'short name' and the PSSM ID, but I haven't yet found a way to map to PDB or interpro ID.

Any suggestions?

Many thanks,

Ben

pssm • 2.0k views
ADD COMMENTlink written 7.2 years ago by ben.readhead20
1
gravatar for ben.readhead
7.2 years ago by
ben.readhead20
ben.readhead20 wrote:

In case anyone comes up against this issue in the future, here's a couple of approaches that the NCBI user services were able to provide:

  1. you can download the FTP file: fasta.tar.gz which contains sequence alignments from the CDs in mFASTA format and parse out the PDB IDs from the FASTA definition lines.

or

  1. you can use the Entrez Utilities to do an ELink from CDD to Structure, and then an ESummary retrieval to get the PDB IDs. For more information about the EUtilities, see: http://www.ncbi.nlm.nih.gov/books/NBK25501/ .

...I've gone with option 1 & it's worked well

cheers

Ben

ADD COMMENTlink written 7.2 years ago by ben.readhead20

thanks for this and strange no one needed this before apparently. just a short addition, the file is here ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/fasta.tar.gz (just took some time to notice you were referring to the link in your question) and the aligned sequences are I believe the same CODs reported by different studies from different organisms, some no longer exist in NCBI database, and as I am working on newly sequenced organisms, not clear which of those GIs I should select to use in GO, but I'll go for the first ones

ADD REPLYlink written 2.4 years ago by FatihSarigol120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1540 users visited in the last hour