I have sequencing data from unidentified parasites in one family tested for. I blasted my sequences in NCBI blast database and have the 'closest blast matches'. For 9 sequences, the highest match is 99%, but total scores vary. Can I for sure identify my sequences as the same genus as these matches? For one other sequence, the top match is 98%. I heard 99% or above is cutoff for genus identification. If I can't identify this one to genus, how do I report the family name of the sequence when I submit my sequence to GenBank? I was told "family name" spp. is not correct, but not sure what is correct. Any help is appreciated!
PS, I also have made a phylogenetic tree, I think my species are novel, so probably can't identify to species level. Do I need to refer to the branching for genus identification of my sequences as well? It supports most of the blast match genus results, but 2. These two are shown to be different genera than the 99% closest match in BLAST. Also due to trimming my alignment, now a unique sequence with 98% match, appears equal to 3 other sequences in my tree.
First, sort your BLAST searches based on %identity - the total score "E value" is not the best sorting method for these type of searches. From what you describe, BLAST will not give you the information you need. It sounds like you have phylogenetic skills, so I highly recommend downloading the relevant sequences, assessing their quality, and then using them for a phylogeny. If your isolates are taxonomically novel, the phylogeny will be more informative than any binomials regardless.
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