No hits found

Question

[coreyhowe99]

Bioinformatics noob here,

I'm working with a firefly database. I have downloaded the blast executables and made a local database with the makeblastdb command. To test the database I have used the blastn command using a luciferase gene as the query, which I know is in the database because I have blasted before in a different program, and I get No hits found. I have tried this with several different luciferase sequences and each time I am getting No hits found.

Does anyone have any idea as to why this is happening? Do I have to change any search parameters?

[GouthamAtla]

Take few sequences and do a online blast and see what kind of hits you get. If the hits are of low confidence, you need to change the stringency parameters in local blast.

[coreyhowe99]

I blasted 6 random sequences from the database and every one said "no significant similarity found" except for one sequence that had several hits with the best one having Query cover: 12% and identity: 99%. I know that there is not any firefly genome or transcriptome that is published online so that might be why I am not getting many hits.

Answer 1

[Michael]

You won't normally find detectable similarity across species on the DNA level, except for RNA genes and repetitive elements or very closely related species. You are not getting any hits, because your query is most likely not in the database because the species is not represented. You should use protein sequence queries and a protein database for this reason if possible, or, if only DNA sequence is available, use tblastx, this was probably used when you found hits earlier.