A typical strategy for verifying a potential ortholog is to use a reciprocal BLAST. Lars describes this in detail in Blast/Reblast to verify homologies so I won't cover it here.
If instead you are trying to get confirmation of the robustness of the BLAST result, then options such as trying alternative search methods (e.g. FASTA and Smith-Waterman), and varying the parameters of the search are possible strategies. Given that you are using protein coding nucleotide sequences, try switch to protein space, so use blastx and equivalents and confirm your nucleotide results against the protein databases. Look at other databases, since you are talking about RefSeq I assume you did your BLAST at NCBI so also have a look at the databases offered elsewhere, e.g. EMBL-EBI, DDBJ, Ensembl, etc.
modified 13 months ago
RamRS ♦ 30k
8.7 years ago by
Hamish • 3.1k