Final answer:
When using a nucleotide BLAST search, a DNA sequence pasted for comparison should not include associated introns, regulatory sequences, or other non-coding DNA sometimes called "junk" DNA. These elements are typically not helpful for identifying gene coding sequences in the BLAST database.
Step-by-step explanation:
When pasting a DNA sequence into the text box for comparison against the human genome using a nucleotide BLAST search, the sequence should not include associated introns and regulatory sequences, genes that encode other RNA molecules, or other DNA sequences sometimes referred to as "junk" DNA. Introns and regulatory sequences are not part of the coding region of genes and do not typically aid in the identification of the gene itself during a BLAST search. Moreover, repetitive or "junk" DNA, while not fully understood in terms of their function, does come with an energy cost for maintenance and may not provide useful information for a BLAST query meant to identify gene coding sequences.
To perform a nucleotide BLAST search, you would navigate to the BLAST search page, click "Nucleotide BLAST", and paste the DNA sequence in question into the "Enter Query Sequence" window. After specifying the species, such as "human" or "Homo sapiens", and initiating the search by clicking "BLAST", the sequence would be compared against known human genome sequences. The output will show where in the human genome the sequence is found and may include links to additional information and graphical views of the genome.