BLASTN

BLASTN is a nucleotide-nucleotide sequence alignment tool within the NCBI BLAST suite. It compares a nucleotide query sequence against a nucleotide database to identify similar regions and potential homologs.

The algorithm uses a seed-and-extend approach. It searches for short exact matches, or words, between the query and database sequences and then extends those matches to form high-scoring local alignments. The scoring considers matches and mismatches, as well as gaps with penalties; results are reported with statistics such as alignment length, percent identity, and an E-value, which estimates the expected number of similar matches that could arise by chance. The default word size and scoring parameters balance speed and sensitivity; users can adjust word size, gap penalties, and other settings.

Input and outputs: The query must be a nucleotide sequence (DNA or RNA). The search is performed against a nucleotide database, such as the NCBI nt database or a user-specified file. BLASTN produces a list of high-scoring segment pairs (HSPs) with pairwise alignments, along with summary statistics and links to the corresponding database entries. Results can be filtered, sorted, and exported in several formats.

Variants and use cases: BLASTN includes standard BLASTN and optimized variants such as discontiguous megablast for more distant relationships or megablast for large, highly similar sequences. Common applications include gene identification, annotation transfer, detection of conserved domains, species identification, and contamination screening. Limitations include reduced sensitivity for very short queries or highly rearranged sequences, and the need to interpret E-values within the context of database size.

Availability: BLASTN is part of the NCBI BLAST+ toolkit and is accessible via the NCBI BLAST web interface as well as command-line tools for local searches.