BLAST is a suite of alignment programs. I agree the relevance of BLASTN is not what it was during the Sanger era, but if you're looking to align a protein-coding sequence it is always better to do so in a translationally-aware (i.e. amino acids) manner - that's what the BLAST suite allows.

Program          Subject             Query
BLASTN           Nucleotide          Nucleotide
BLASTP           Protein             Protein
BLASTX           Protein             Protein
TBLASTN          Protein             Protein
TBLASTX          Protein             Protein

I could think of many distinct cases (>30) where I have used BLAST. It was not always the best tool for a given task, but it is almost always the fastest.

Rather than going through my exotic examples, I encourage you to think about other tools that rely on BLAST. For example, it is heavily used in proteomics. I feel confident in saying that more than 50% of machine learning applications aiming to predict something about proteins rely on BLAST. That's because BLAST has been the fastest tool for so long to make PSSM matrices (or alignment checkpoints, depending on one's preference). Even though there are tools today with comparable speed to BLAST for that purpose, they are either relatively recent or simply are not as widespread.

I use it to quickly map any kind of sequence to a reference or to quickly find/group together similar sequences. For example, I use blast to:

• map siRNAs to target transcripts
• identify/validate CRISPR/Cas9 target sites
• map mass spectrometry identified peptides to proteins
• collect similar sequences before building a multiple sequence alignment

One of my own practical examples that I was using in South America with some colleagues: we performed RNA-seq of a bacterial strain and assembled the transcriptome to identify candidate mRNA sequences with coding potential. We then ran these sequences through blastx to assist in the interpretation of their function.

In the past, in a clinical setting in the UK NHS (National Health Service), I also downloaded a local copy of the nt BLAST database and aligned samples against it to check for contamination.

Kevin