Which hit do I select from my BLASTN result when all of them have the same statistics?

Question

[amulyabaral2]

Hi all, I am doing BLASTN to look for AMR genes in my contigs assembled from shotgun metagenome sequence reads. The BLAST results show the same query sequence matching against different variants of a same gene; all of them with the same stats as shown in the example below. What would be the best approach going forward in this scenario? Do I just group all of them as a single hit to the OXA gene (despite the differences between the variants) , or consider each hit as an individual match and include all of them in my results?

[GenoMax]

Please do not delete posts once they have received at least one comment/answer. While you may have resolved your question this thread may help future users.

[Dunois]

The top 10 hits are all OXA genes, and the matches are all significant, high subject coverage, and high identity. But the query coverage isn't as high -- only positions 107 through 934 are aligned, but the sequence has another 900 bases left. So it appears that at the very least this sequence is an OXA-something.

You could search against a more general database also (I presume your subject database is enriched for AMR sequences?) to see if something comes up that matches the remainder of the sequence.

Answer 1

[Istvan Albert]

Sounds like your subject sequences are identical - the data might be redundant.

In any case, you should reverse the question instead - does it matter which one you pick? The answer to that question will decide which one to pick.

Answer 2

[GenoMax]

What database are you blasting against? Clearly there is a lot of redundancy in that database which is why you get nearly identical hits from multiple sequences (are these genomes)? If you simply want to know if your query is X gene (OXA in this case) then it does not matter which hit you choose.