I am planning to set up and maintain a local version of the NR and other NCBI databases, for running in-house BLAST searches. I would also like to my local version of the databases be in synch with NCBI through regular updates. NCBI suggests using the update_blastdb.pl (http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl) to download the latest versions of all the pre-formatted databases. Does anyone have experiences to share on using this script? Are there alternative solutions? Will appreciate everyone's feedback. Thanks, Anjan
It's fine to constantly update the blast databases, but then you need to document which release you used when you did your analysis, right? With a new database, you might get slightly different hits...
ah yes, i believe running fastacmd with a -I option returns the version of the database. so fastacmd -d $HOME/blastdb/nt -I returns the version of the nt databases. This output can easily be tacked onto the end of a blast report to keep track of the database version.
+1 @flxlex: Agree. Was think the first thing any script should do is get and log the version database used before pulling data.
+1 @flxlex: Agree, the first thing any script should do is get and log the version database used before pulling data; or for that matter any data source.
I like the idea of maintaining a log of updates. The script does not create one. However it should not be difficult to start a log.
@Anjan: The idea is not to log the updates, store the version of BLAST the result were created with in the result set, or at least this is what I meant. If you have any questions, just comment again. Cheers!
[EDIT] @Anjan: The idea is not to log the updates when installed, but to store the version of BLAST used to produce the results with result data created. If you have any questions, just comment again. Cheers!
+1 @Anjan: Cool, thanks for posting the command-lines, and glad you were able to figure out what I was trying to say. Cheers!
You may want to try this: http://www.dnabaser.com/download/NCBI-BLAST-downloader/