Thursday, 24 February 2011

Plan to automate miRbase

Need to check for a new release of miRbase and then download it

It is located at:

Need to check the data-stamp on the directory that CURRENT points to and then download it if it is newer than the date-stamp of the last update on the local machine. On average 6 monthly.

Need to get the mature.fa.gz file from this directory

Then this needs to be moved to the local /usr/share/ncbi/data directory
Then it needs to be gunziped
Then it needs to be converted to a blast database with the formatdb command.

Grep gga from mature.fa > gga_mature.fa selects out those from Gallus gallus.

To use
megablast -d /usr/share/ncbi/data/mature.fa -i sequences.fa -o sequences.out -W 7 -D 2 -p 100 [-e 1000]