Lab Exercise $-$ Practical $08-$ part $2$

Question $2$:

With the given Sequence X $($check the next slide$),$ answers the question below accordingly.

a$)$ Translate the nucleotide sequence into a protein sequence by using the appropriate EMBOSS Tool or Program. Provide the name of the program used and the translated sequence.

b$)$ Using the translated sequence, conduct protein BLAST search against reference proteins and Protein Data Bank databases. Answer the following questions accordingly:

i$.$ How many sequence obtained from each of the database?

ii$.$ Obtain general information based from the first hits for each of the databaseGeneral Questions

What is the default substitution matrix used by protein BLAST? List out the other available substitution matrix.

State two parameters that would influence the obtained $E$ value from BLAST search

Is BLAST only employed in NCBI's databases? Briefly explain.