CrocoBLAST is built to help you plan your BLAST jobs and run them efficiently. CrocoBLAST operates with the concept of queue, which is basically a list of BLAST jobs scheduled to run. Thus, you can plan several BLAST job and let CrocoBLAST manage their execution for you.
All CrocoBLAST functionality is available via the command line utility and the graphical user interface. In fact, the graphical user interface does precisely what its name suggests: it provides an interface for the command line utility. In a nutshell, while you can interact with CrocoBLAST via simple commands, you may also use the interface to generate the commands or read the output of such commands.
As already mentioned, BLAST takes an input file with unknown sequences and aligns each such sequence against a database of known sequences. Therefore, to submit a BLAST job, you must specify which database you wish to align against. The first time you indicate a database for a BLAST job, CrocoBLAST will remember it and add it to its index, so that in the future it is easier for you to access this database. You can see which databases are already indexed in CrocoBLAST:
You can provide a simple name for each database, that you may later refer to whenever you need to run a BLAST job. There are two ways to add a new database to the CrocoBLAST index.
Retrieve database from NCBI servers
In the most typical scenario, you will use the established reference sequence databases maintained by NCBI. CrocoBLAST allows you to specify the name of such a database, and will download or update the database for you:
CrocoBLAST -add_database --ncbi_download ncbi_database_name output_folder
CrocoBLAST -update_ncbi_database ncbi_database_name output_folder
When adding or updating a database in this manner, you need not worry about the format of the database, as NCBI provides pre-formatted database files.
Add database from your computer
Say you have created one or more BLAST jobs and are ready to start munching some sequences. It's easy:
When you run CrocoBLAST this way, you will make the most efficient use of your computational resources, as CrocoBLAST will figure out how to best parallelize the calculation on your machine. Nonetheless, if you want to limit the calculation to fewer cores, you may do so:
CrocoBLAST -run --num_threads number_of_threads
Similarly, you can easily stop or pause the execution at any time.
If you wish to resume the calculation, simply tell CrocoBLAST to start munching. It will automatically detect the current state of each job in the queue, and continue from where it left off.
While CrocoBLAST operates with the concept of queue, it is important to note that only one job is active at any given time. You can check the current state of the CrocoBLAST queue:
This will provide you with information regarding which jobs are queued, with full details regarding the BLAST setup, as well as a description about the progress of the alignment.