Question

What General Parameters should you set when you perform the BLASTN search?

Answer 1

When performing a BLASTN search, you should set parameters such as the search set/database, program selection, word size, and expect value (E-value).

Step-by-step explanation:

When performing a BLASTN search, there are several general parameters that you should set:

1. Choose the Search Set/Database:Select the database or database subset that you want to search against. For example, you can choose the NR database which contains non-redundant sequences from GenBank and other sources.
2. Program Selection: Select the appropriate program for your search. For BLASTN, you would select the nucleotide-nucleotide BLAST program.
3. Word Size: Set the word size, which represents the length of the sequences that are compared at a time. The default word size for BLASTN is 11, but you can adjust it if needed.
4. Expect Value (E-value): Set the significance threshold to filter out random matches. A lower E-value indicates a more significant match.