Nucleotide vs nucleotide search can be used to identify the input sequences, find related sequences, map mRNA to its genomic counterpart, and map primers to their annealing target. The following command line searches the input nucleotide query in my_query file against the nt database using megablast algorithm with word size set to 56. The results are saved in my_output:
blastall -p blastn -i my_query -d nt -n T -W 56 -o my_output
The -n T and -W 56 increase the stringency and the speed of the search. It works best for matching highly similar sequences with reasonable length - such as in prelimiary mapping mRNAs to their genomic counterparts. Note that we should not attempt to map the detailedexon/intron boundaries using blastall. Instead we should use specialized tools such as spidey and splign. See more details at:
http://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/Spidey/
http://www.ncbi.nlm.nih.gov/sutils/splign/.