Practice question
Question
In sequence alignment by BLAST, each word from query sequence is typically _______ residues for protein sequences and _______ residues for DNA sequences.
Explanation
BLAST accelerates alignment using short word seeds to find initial matches. For proteins default word size is three amino acids, balancing sensitivity and speed given 20-letter alphabet. For DNA, longer eleven-nucleotide seeds are used because four-letter alphabet would generate excessive random hits otherwise.
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