Discrepancy in Nucleotide and CDS (Amino acid) Sequence allignments??

10 October 2019 1 3K Report

For nucleotide sequence submission to NCBI, the amino acid sequence are also needed to be provided. I did the BLAST in which I got 100% sequence similarity with 0 gaps with subject sequence. However, when I applied the CDS option, I am getting many differences in the query and subject sequence. Also getting * (stop codons) in the query sequence which are absent in the subject sequence. Wanted to how can I resolve this issue and submit my sequence.

Amit V Pandey

I also think the reason is an incorrect setting for the first codon.

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