2.1.3 Setup

To ensure the smooth execution of blast programs, we need to set up a BLAST configuration file, named ncbi.ini to instruct blast the location of the data directory and db directory. In the above setup, the path to data directory and db directory should be specified the following way:

[NCBI]

DATA=E:\blast-2.2.15\data

[BLAST]

BLASTDB=E:\blast-2.2.15\db

Users can use the following steps to create this file on PC:

• launch notepad
• copy paste the above lines in blue
• modify the path (E:\blast-2.2.15\) to reflect the actual setup
• name the file as ncbi.ini using "save as" and double quote the name to prevent Windows from adding the .txt extension

We need to place the resulted ncbi.ini file under the Windows directory. BLAST programs will read this file upon start to get the path information it needs during the search.

Note that matrices are hard-coded in newer version of BLAST (2.2.13 and latter). With -V F setting, default since 2.2.14, blastall will no longer need to read the matrix information from an outside file. We should still specify the path to data directory just in case we need to use the old engine (-V T setting). In addition, firewall configuration related to NCBI programs, such as blastcl3, will need to be stored in this ncbi.ini file. See Appendix for more information (Section ###).