Final answer:
For a nucleotide query, the appropriate BLASTN database to search first is the nt (nucleotide collection) database. This database is comprehensive and suitable for comparing nucleotide sequences from a variety of organisms. Other databases like nr, pdb, and refseq_genomic serve different purposes related to protein sequences and structures.
Step-by-step explanation:
When choosing which BLASTN database to search first, it is important to match the type of sequence you are querying with the appropriate database. If you are working with a nucleotide sequence, you should begin with the nt (nucleotide collection) database. This database contains a comprehensive collection of nucleotide sequences from a variety of organisms and is suitable for comparing your nucleotide sequence to others that have been collected and annotated.
The other databases, such as nr (non-redundant protein sequences), pdb (protein data bank), and refseq_genomic (reference genomic sequences) have specific uses as well. The nr database would be used for protein sequences, pdb for three-dimensional protein structures, and refseq_genomic for reference genomic sequences. Therefore, option A) nt is the correct choice for a nucleotide query.
To utilize BLAST, one would go to the NCBI BLAST website, select nucleotide blast, and enter their query sequence. The results from BLAST will provide insights into how your sequence compares to others and can be instrumental in studies involving gene function, evolutionary relationships, and identifying species