How Did BLAST Work?
Query Parsing for Nucleotide-Nucleotide Searches
(using blastn as an example algorithm)
- the blastn algorithm parses nucleotide sequences into 11 letter "words"
(as noted in the earlier slide on nucleotide BLAST, word size varies among the different nucleotide BLAST algorithms)
- do the same for every sequence in the query database
- identify database sequences with exact word matches
- extend the sequence comparison between your query and the hit in both directions
- report the hit in the search results if it meets or exceeds the BLAST cutoffs for a statistically significant match
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