A forward primer sequence for a 16S rRNA gene on BLAST shows identification with Strenotrophomonas maltophilia having the following output for the first four matches:
Gap Max score Total score Query cover E value Max ident
Seq1 0% 673 673 99% 0.0 88%
Seq2 0% 673 673 99% 0.0 88%
Seq3 0% 673 673 99% 0.0 88%
Seq4 0% 673 673 99% 0.0 88%
The reverse primer for the same sequence yields:
Seq1 0% 678 678 99% 0.0 86%
Seq2 0% 676 676 99% 0.0 85%
Seq3 0% 675 675 99% 0.0 85%
Seq4 0% 673 673 99% 0.0 85%
The generated contig for the sequence using the reverse complement yields similar output.
Gap percentage 0% and E value 0.0 shows that the BLAST result is not by chance alone and organism Strephomonas maltophilia is being identified for the sequence. but so much less identity is shown in major variation in the 16S rRNA gene.
I am not being able to infer the result. Can anyone help me infer the result and submission for NCBI GenBank? Does this result point to new strain identification. I am a novice in sequence analysis and request your suggestions.
It's not easy to interpret BLAST if you are not experienced. Your results suggest that your sequence is only 85-88% identical to Stenotrophomonas sequences (assuming that all 4 sequences were deposited as that species). Because Genbank has many, many 16S rRNA sequences, such a low percentage is very unusual. Most 16S rRNA reads will have higher identity scores, and a value below 90% is only found for very novel, previously never seen bacterial species.
Are you sure that the quality of your DNA sequences is good? That would be a very likely explanation of low identity scores.
If you like, I'd be happy to take a closer look - you can send me the chromatograms and fasta files privately.
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