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How does increasing or decreasing the word length parameter affect the run time and results for...

How does increasing or decreasing the word length parameter affect the run time and results for BLAST?

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Answer #1

BLAST is Basic Local Alignment Search Tool . It is both an algorithm and programme which is used to compare primary sequence of proteins, DNA etc.

BLAST searches for perfect sequence match length of given word size.

Increasing the word length will result in lesser hits as it is necessary to have long continuous sequences of exact match.

Decresing the word length will result in more reliable homologous sequences (hits) .

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