. (a) 1pt What is the advantage of a seeded method like BLAST compared to a Need
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. (a) 1pt What is the advantage of a seeded method like BLAST compared to a Needleman-Wunsch alignment? (b) 3pt Which favor of BLAST is most sensitive for comparing your sequence to a species that are NOT closely related? Explain in one sentence. (c) 3pt In Karlin-Altshul statistics, what are four main assumptions? (d) 3pt Describe a scenario where BLAST will be incapable of finding a high quality match, even when one exists in the database. To get full credit, you must specify the word hit length utilized by BLAST in your scenario AND state the actual percent identity of your query to the best sequence in the database (which BLAST is unable to find)Explanation / Answer
a.The global (nedleamann and wounch ) alignment technique align sequence end to end, entire sequence from starting to end, hence it is used in homologous gene or protein comparison in different species. Where as local alignment as like BLAS is more advantageous over global alignment because it aligns sequences with highest level of similarities and because of that it is used in conserved sequence alignment study.
b. Protein BLAST is most sensitive for species that are not closely related because BLAST can align local search, which are conserved sequences.
c. Karlin-Altschul makes 4 main assumption that,
A positive score must be positive,
Alignment don’t contain gaps
The sequences are indefinitely long
Expected score must be negative
The letter of the sequences are independent and indentically distributed
d. BLAST will be incapable of finding the high quality of match in case of long sequences because it can align or search single query at a time hence we can not compare many species at once. We can align short sequences up to 30 in BLAST
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