Editing CrocoBLAST:UserManual (section)

=1. Input file and Database=
It its essence, BLAST aligns a set of nucleotide or protein sequences (''input file'') against a set of reference sequences (''database''), reporting the score for each alignment in an effort to help you identify the closest matches to the given input sequences. In practice, this translates into taking an ''input file'' with many query sequences, and aligning each of the query sequences against a ''database'' of known sequences. Such databases are typically stored in suitable repositories such as NCBI, or may be obtained in-house.

Therefore, in order to run BLAST, you will need to specify an ''input file'' containing the query sequences, and a ''database file'' containing the reference sequences. CrocoBLAST accepts input files in FASTA and FASTQ format. BLAST uses a specific ''database format'' for database file. For including a ''database'' in CrocoBLAST, you may indicate provide a database file either in the BLAST ''database format'' or in FASTA or FASTQ format, which will be converted to database format before BLAST is run. Further CrocoBLAST allows you to directly download and update databases from the NCBI server.