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ing questions. a. What does BLAST do and how is it useful for your experiment? b. How does BLAST calculate the maximum score? c. How does BLAST calculate the query coverage? d. How does BLAST calculate the E-value?

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Answer #1

Answer:
1.
The BLAST(Basic Local Alignment Search Tool detect the local similar areas between sequences. It is used to make comparison between sequences of nucleotide or protein and databases of sequence. It makes calculation of the significance of matches.
2.max score is calculated by BLAST by calculating highest alignment score between the sequence segment of database & query sequence.
3. Query coverage is calculated by BLAST by calculating query length percentage that is consisted in the aligned piece. It is calculated over total score or all segments.

4. E-value are value of alignments predicted by chance with a specific score. e
E-value is inversely proportional to significance of score.
Equation:
E-val = P-val * N

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