Editing CrocoBLAST:UserManual (section)

== 2.3. Adding  a database from a FASTA/FASTQ sequence file in your computer ==
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 refer to the databases later. When your database is in FASTA or FASTQ format, you will need to tell CrocoBLAST the '''type of sequence''' it will find in the file:

# <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></code>
# <code>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></code>
# <code>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></code>
# <code>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>

Using this command will create a database entry named "database_name" in CrocoBLAST.

Formatted BLAST database files will be generated in the specified output folder.