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Version of UniProt and Pfam databases #37

Open GatorShan opened 4 years ago

GatorShan commented 4 years ago

Dear Brian,

Is there a way to check the version of the UniProt and Pfam databases that I downloaded?

The script Build_Trinotate_Boilerplate_SQLite_db.pl from Trinotate version 3.0.1 was used to download the databases.

I am writing a manuscript, and these informations would be helpful.

Thanks!!

Shan

brianjohnhaas commented 4 years ago

Hi Shan,

When you run the boilerplate database generation step, it does a pull-down of whatever version of sprot is available at that very moment. You could probably just look at the datestamp of the files that were generated at that time and it should be a good indicator. I don't know if the versioning info is embedded in the files that are downloaded, but that could be a good place to look too.

best,

~b

On Wed, May 20, 2020 at 1:38 PM Shengchen Shan notifications@github.com wrote:

Dear Brian,

Is there a way to check the version of the UniProt and Pfam databases that I downloaded?

The script Build_Trinotate_Boilerplate_SQLite_db.pl from Trinotate version 3.0.1 was used to download the databases.

I am writing a manuscript, and these informations would be helpful.

Thanks!!

Shan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/37, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX24BJBKNGAUQJDYMNDRSQIRDANCNFSM4NGFMD7A .

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

GatorShan commented 4 years ago

Hi Brian,

Thanks for your quick response!

I just checked the release histories of the two databases, and I think I can infer the version based on this info as you mentioned.

UniProt: ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases Pfam: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/

Thanks again!

Shan

brianjohnhaas commented 4 years ago

great!

On Wed, May 20, 2020 at 2:46 PM Shengchen Shan notifications@github.com wrote:

Hi Brian,

Thanks for your quick response!

I just checked the release histories of the two databases, and I think I can infer the version based on this info as you mentioned.

UniProt: ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases Pfam: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/

Thanks again!

Shan

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/37#issuecomment-631656488, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZ3HN7I6CWEIHNGCGDRSQQQTANCNFSM4NGFMD7A .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas