Editing CrocoBLAST:Terminology (section)

=Input file and Database=
It its essence, BLAST takes an unknown nucleotide or protein sequence, tries to align it against a set of reference sequences, and then reports the score of each alignment, in an effort to help you identify the unknown sequence. 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. You may indicate the database file either in database format or in FASTA or FASTQ format, which will be converted to database format before BLAST is run. Within CrocoBLAST you may directly download databases from the NCBI server.