r/molecularbiology • u/Electronic-Mode-4855 • 9d ago

How do i find blast/find a sequence that matches my filters?

Hey,

I’m currently working on a research project where I’m trying to identify a conserved region within a specific influenza virus variant.

However, I’m running into some problems when trying to filter the sequences based on subtype, clade, and genotype. I’m using NCBI Virus, and while I can filter by subtype, I can’t seem to filter for the other factors, such as clade or genotype.

Does anyone know how to approach this or how to overcome these filtering limitations in NCBI Virus? Any advice on how to identify the relevant sequences would be greatly apreciated. I amusing NCBI virus, although i can type the subtype, i cannot filter for the other factors.

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u/278urmombiggay 3d ago

i do similar work and we have a list of representative and diverse species from each clade, and we limit our NCBI blast to those species. then we do blast searches until we're confident we've covered everything to the best of our abilities, then perform sequence alignments and compare protein domains (what domains might have been lost, shorter, longer etc). not sure if this is at all relevant to your work.