I am working on WD protein, which nucleotide sequence was obtained after sequencing. When I proceeded for sequence alighnment to check the most similar homologs, I have found that result of BLASTn is showing maximum similarity with WD-55 and BLASTp with WD-4 respectively. Which result should i follow?
Hi Lakee Sharma ,
If I understand correctly, you sequenced WD coding region, tried to BLAST, and the BLASTn & BLASTp results refer topartial different proteins.
- Have you annotated your sequence according to BLASTn?
- Have you checked that any introns do you have?
- Might you have a partially sequence of the gene?
- Any UTR?
- While translating your DNA sequence, be sure that you choose the right frame.
- While performing BLASTn, choose CDS feature of NCBI. It shows the CDS of your DNA sequence.
Good luck.
Kaan Hürkan I was referring to the questioner. Since there is no such information given in the question.
@Abhijeet Singh, I have firstly done the blastn of nucleotide sequence and then translated it and longest amino acid sequence was done with blastp.
Lakee Sharma in the case you have used the longest aa sequence (in frame and without internal stop codons), blastp results would be better and more convincing to believe i.e. "BLASTp with WD-4"
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