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114 DateThis step creates additional files with the same name, but with differentextensions such as “.pin” and “.psq.” All possible formatdb parameters can beviewed with the ‘-- help’ flag. After this step, the original file myDatabaseFileis no longer needed by BLAST for sequence comparison; however, this fileshould be maintained if disk space availability is not an issue. Once the databasefile is formatted, it is ready for use by BLAST.3.1.3. Running BLAST for All Proteins in the Query SetIndividual amino acid sequences in the query set are compared with the databaseof reference genomes in a sequential manner, using the wrapper programdescribed in Subheading 2.2. The following is a simple example of the BLASTcommand executed from within the wrapper script (with the wrapper scriptwritten in the PERL language; for PERL, see http://www. perlfoundation.org/):% perl /path/to/wrapper/myBlastWrapper.pl –imyInputFile –d myDatabase File –b /path/to/BLAST/executable–p myBlastParser.plDetails of the options used for the wrapper program are as follows:−i−d−b−pName of the input file containing query protein sequencesName of the reference genome database to useThe directory where the BLAST programs are locatedThe BLAST results parser program to useUsers are free to select and set more options based on the tasks ascribed tothe wrapper program. Information about various BLAST options can beobtained using the ‘-- help’ flag.The primary job of the wrapper program is to execute BLAST for each inputsequence, and store the output such that it can be retrieved with a unique identifier.The output can either be stored separately as results of each comparison,or jointly, based on the configuration of the wrapper program. In addition, asmentioned previously, other steps of the protocol such as parsing BLASTresults can also be executed from within the wrapper, greatly reducing the complexityand size of the output. In the author’s experience, computational efficiencyis high if the wrapper program couples the BLAST step with the parserstep, and stores the parsed output for all input sequences in a single text file.The following pseudocode describes this approach.open myInputFile;foreach querySequence j {system “blastall –p blastp –i querySequence –dmyDatabaseFile –o myBLASTOutputForProtein_j”;