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What is an e-value

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Assignment:

You decide to explore this particular sequence.

You want to determine if it is known and/or what protein sequences in other plants it might be similar to?

You decide to perform a BLAST search against the "Reference Proteins (refseq_protein)" database for "Organism" = "plants (taxid:3193)".

Question a. What is BLAST? Describe the algorithm, discuss what a HSP is.

Basic Local Alignment Search Tool: used to compare sequences and identify similarities. High-Scoring Segment Pair: align sequences where there are high degree of similarities

Question b. What is an E-value? How is it determined? What is considered a significant E-value for DNA BLAST Hits vs. PROTEIN BLAST Hits?

E-value (Expected Value): chance that the alignment is random. The lower the e-value the more significant it is. The E-value for a DNA BLAST is <1e-5; and Protein BLAST is <1e-3.

Question c. What is the difference and advantages of running BLAST using the blastx vs. blastn algorithm?

Blastx:

Blastn:

Question d. After running blast on the expressed sequence, how many sequences are returned with a significant E-value?

Question e. For the significant results returned, what non-hypothetical non-predicted gene is likely being coded for by the sequence you performed blast on?

Question f.  For the significant results returned, what is the translation frame that the protein for the gene is likely being generated from?

Reference no: EM133913254

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