Question: Converting Gis Between Genbank And .Ptt Files
0
gravatar for Admiral
7.9 years ago by
Admiral0
Admiral0 wrote:

I'm using both genbank files (downloaded from NCBI ftp) and the corresponding .ptt files (available as all.pt.tar.gz here).

However, while each gene is identified with a GI in both of the files, they do not match. As one example, here's the genbank and ptt files of the same Acaryochloris marina chromosome. The AM10003 locus is identified with 158333234 in the ptt file, and 158303475 in the genbank file. (Searching for AM10003 in NCBI gets me to both of those IDs as well).

How can I convert from the genbank ID to the ptt ID, or vice versa? (I have to do this for an extremely large number of genes, so querying NCBI's site for each one's locus tag isn't a practical option).

genbank conversion • 3.5k views
ADD COMMENTlink modified 2.9 years ago by Ranjit0 • written 7.9 years ago by Admiral0
1
gravatar for Vikas Bansal
7.9 years ago by
Vikas Bansal2.4k
Berlin, Germany
Vikas Bansal2.4k wrote:

This is because you have not opened the corresponding .ptt file for genbank file. In the ftp address bar check the uid and file name. I think both of the files should be in same directory. For your genbank file, here is the .ptt file and for your ptt file, here is your genbank file.

ADD COMMENTlink written 7.9 years ago by Vikas Bansal2.4k

Excellent- thanks. Just one more question- do you know if there is a file containing all PTTs for my version of the genbank files, analogous to ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.ptt.tar.gz? Or should I download them individually?

ADD REPLYlink written 7.9 years ago by Admiral0

You have to download them individually. You can simply download all the files by linux command - wget ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Acaryochloris_marina_MBIC11017_uid12997/*.ptt

ADD REPLYlink written 7.9 years ago by Vikas Bansal2.4k

I actually tried that command, but NCBI appears to throttle such requests so that it can never get more than a few files... I'll try other approaches. Thanks!

ADD REPLYlink written 7.9 years ago by Admiral0
0
gravatar for Ranjit
2.9 years ago by
Ranjit0
Ranjit0 wrote:

check this https://github.com/sgivan/gb2ptt

ADD COMMENTlink written 2.9 years ago by Ranjit0
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