DNA sequences; Protein sequence
A biological sequence is a sequence with a small fixed alphabet, and represents a naturally occurring or experimental generated fragment of genetic or protein material or any intermediate product (like the messenger RNA).
Example: A DNA fragment has the 4 character alphabet ‘A’, ‘C’, ‘T’, ‘G’. Chromosomes are long strings over this alphabet.
Biological sequences can be long. A full chromosome may have millions of characters. Therefore development of proper storing and indexing strategies is very important for fast retrieval. Suffix tree based indexes have been used successfully for long biological sequences. Further, approximate string matching techniques with potential deletions and insertions are important for biological sequences. BLAST is a well known algorithm used for approximate matching and ranking of biological sequences.
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