This feature is similar in principle, but different in implementation, to that found in megablast. It allows query concatenation for non-megablast blastn or tblastn searches and reduces the time needed for the search since the database is scanned only once. It should not be combined with -g F. The argument to -B option must be equal to the number of sequences in the FASTA input file.
When the -B option is used, the results may differ from the ones produced with individual queries due to the heuristic nature of BLAST. It is guaranteed that matching sequences will appear in the same order when they are tied in e value and are part of the output both with and without -B. When the -B option is used, the summary statistics at the bottom of the output are for the combined set of queries, not tabulated for the individual queries in a multiple-query input.
The parameter -B is obsolete since the new BLAST engine will concatenate queries automatically. Users should not attemopt to combine -B with the new BLAST engine (-V F). See 3.2.42 for more information on new BLAST engine.