[BiO BB] pfam

[Dan Bolser]

On 30/03/07, Divya P Syamala <divyaps at ncbs.res.in> wrote:
> hi all,
>  I have been trying to download some information from Pfam database.I
> couldn't figure out what the titles for the downloaded information from
> the following links are:

Dude... did you read the README? It points to the following page;

http://www.sanger.ac.uk/Software/Pfam/help/rdb_doc.shtml


This doesn't directly give a list of column id's and descriptions but
does give enough information for you to get going with the database.
The columns (and files) should at least become easier to understand
once you have read that page.


> ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/architecture.txt.gz
> ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/pfamA_architecture.txt.gz
> ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/pfamseq_architecture.txt.gz
>
> Secondly I would like to know how to get the taxonomy information for a list
> of genebank ids.

If you read the above you will see that taxonomic information is
included in the pfam database. However, to answer your question, you
can get that data from here...

Dang... things keep moving around! Or perhaps I just forgot... the
file 'gi_taxid_nucl.dmp' is what you need and it is under here...

ftp://ftp.ncbi.nih.gov/pub/taxonomy/


Google also shows a number of API services that serve up this mapping.


> Thanks in advance
> divya
>
>
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