Question: Query Genbank Using A Mysql Interface
0
gravatar for arronslacey
6.5 years ago by
arronslacey260
United Kingdom
arronslacey260 wrote:

Hi - how can I query genbank using a mysql type interface, so that I can bring back sequences of interest based on a sub-string of the Definition field? or what is the least painful way to download all proteins in genbank and put them into a mysql file? even just download the flat file database and I can work out the rest from there.

thanks

mysql genbank • 3.0k views
ADD COMMENTlink modified 6.5 years ago by Pierre Lindenbaum127k • written 6.5 years ago by arronslacey260
1
gravatar for Pierre Lindenbaum
6.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

As far as I remember, NCBI uses Sybase(?) ( http://www.ncbi.nlm.nih.gov/books/NBK21081/ outdated ? ) : you cannot query it using a mysql client

. Retrieval of full documents comes from a variety of “back-end” databases, depending on the node. These might be Sybase or Microsoft SQL Server relational databases of a variety of schemas or text files of various formats. Links are supported using the Sybase IQ database product.

You should use the E-Utilities: http://www.ncbi.nlm.nih.gov/books/NBK25500/

or what is the least painful way to download all proteins in genbank and put them into a mysql file

ftp://ftp.ncbi.nih.gov/genbank/

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Pierre Lindenbaum127k
1

NCBI is Microsoft SQL Server.

ADD REPLYlink written 6.5 years ago by wdiwdi380

thanks pierre this is great.

ADD REPLYlink written 6.5 years ago by arronslacey260
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: 2285 users visited in the last hour