Editing CrocoBLAST:Job management (section)

=Manage databases=
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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:

<code>
CrocoBLAST -list_databases
</code>

If you want to remove a database from the CrocoBLAST index (for example, because it has become obsolete), you need to first specify the type of '''sequences''' it holds, and, of course, the name of the database.

<code>
CrocoBLAST -remove_database '''nucleotide''' <span style="color:blue">database_name</span><br>
CrocoBLAST -remove_database '''protein''' <span style="color:blue">database_name</span>
</code>


There are two ways to add a new database to the CrocoBLAST index. In both cases, you should provide a simple name for new each database, so that you may later refer this database easily whenever you need to run a BLAST job. 
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==Retrieve database from the NCBI servers==
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In the most typical scenario, you will use the [ftp://ftp.ncbi.nlm.nih.gov/refseq/release/ 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:

<code>
CrocoBLAST -add_database --ncbi_download <span style="color:blue">ncbi_database_name</span> <span style="color:green">output_folder</span><br>
CrocoBLAST -update_ncbi_database <span style="color:blue">ncbi_database_name</span> <span style="color:green">output_folder</span>
</code>

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.
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==Add database from your computer==
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If you have already downloaded the databases from NCBI, or if you do not have internet connection, you may add to the CrocoBLAST index database files stored on your computer. Remember to provide a unique and representative name for each database you add, so that it is easy to call the databases later. If the database files are appropriately formatted (e.g., psq or nsq):

<code>
CrocoBLAST -add_database --formated_db <span style="color:green">nsq_database_file</span><br>
CrocoBLAST -add_database --formated_db <span style="color:green">psq_database_file</span>
</code>

If your database is in FASTA or FASTQ format, you will need to tell CrocoBLAST the type of '''sequence''' it will find in the database:

<code>
CrocoBLAST -add_database --sequence_file '''nucleotide''' <span style="color:green">fasta_file</span> <span style="color:orange">database_name</span> <span style="color:green">output_folder</span><br>
CrocoBLAST -add_database --sequence_file '''protein''' <span style="color:green">fasta_file</span> <span style="color:orange">database_name</span> <span style="color:green">output_folder</span><br>
CrocoBLAST -add_database --sequence_file '''nucleotide''' <span style="color:green">fastq_file</span> <span style="color:orange">database_name</span> <span style="color:green">output_folder</span><br>
CrocoBLAST -add_database --sequence_file '''protein''' <span style="color:green">fastq_file</span> <span style="color:orange">database_name</span> <span style="color:green">output_folder</span>
</code>
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