Building your database 3 contig import

NOTE: You should perform at least [step 1](Building your database 1 - BLASTP and BLASTN) of building the database before proceeding to this step.

Importing contigs

Contig sequences can be imported into the ITEP database using the setup_step3.sh function.

To import the genome sequences run the following from the $root directory (it will only work if you run it from here):

$ ./setup_step3.sh

It is necessary to run this command if you wish to get the DNA sequences (or their translations) for tBLASTn hits or for other regions of the genome or in order to match up tBLASTn hits with existing called genes (unless you specify the contig IDs in the same manner as they are in the database - append the organism ID to the contig IDs provided in the input Genbank files).

NOTE SQLite has a default maximum string length of 1 billion. If any of your contigs are more than 1 billion base pairs you will not be able to import them without re-compiling SQLite with a larger maximum (see https://www.sqlite.org/limits.html for details)