Actually I have submitted the 16S rna sequence in NCBI for accession number but BLAST similarity search analysis indicates the following sequences may be misassembled:
This could be due to:
- a mixture of plus and minus strand sequence
- incorrect order of the assembled fragments
or
- missing sequence indicated by gaps in BLAST results
Therefore how to rectify the following sequence
ACGGGTGAGTAACACGTGAGAATCTGGCTTCAGGTCGGGGACAACCACTGGAAACGGTGGCTAATACTGGATATGCCGGAAGGTGAAAGATTAATTGCCTGAAGATGAGCTCGCGACTGATTAGCTAGTAGGTGTGGTAAGAGCGCACCTAGGCGACGATCAGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATACCGCGTGAGGGAGGAAGGCTCTTGGGTTGTAAACCTCTTTTCTCAAGGAATAAGAAATGAAGGTACTTGAGGAATAAGCATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGAGTCCGTAGGTGGCGATTCAAGTCTGCTGTCAAAGCACAAGGCTCAACCTTGTAAAGGCAGTGGAAACTGAATGGCTAGAGTGCGTTCGGGGCAGAAGGAATTCCTGGTGTAGCGGTGAAATGCGTAGAGATCAGGAAGAACACCGGTGGCGAAAGCGTGCTGCTAGGCCGCAACTGACGCTGAGGGACGAAAGCTAGGGGAGCGAATGGGATTAGATACCCCAGTAGTCCTAGCCGTAAACGATGGATACTAGGCGTGGCTTGTATCGACCCGAGCCGTGCCGGAGCTAACGCGTTAAGTATCCCGCCTGGGGAGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCAAGACTTGACATGTCGCGAACTTTTCTGAAAGGAAGGGTGCCTTCGGGAGCGCGAACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTTTCTAGTTGCCAGCATTAAGGGTGGGCACTCTAGAGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGCCCCTTACGTCCTGGGCTACACACGTACTACAATGCTACGGACAAAGGGCAGCGACACAGCGATGTGAAGCAATCTCATAAACCGTAGCTCAGTTCAGATCGCAGCTGCAACTCGCCTGCGTGAAGGAGGAATCGCTAGTAATTGCAGGTCAGCATACTGCAGTGAATTCGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGAAG
Hi, I am not sure if there is a way to find out other than repeating the alignment process.
Good luck!
Dear Priti, when I blast your sequence, some gaps and mismatchs were seen on sequence. I advise you first check your raw sequence data using FinchTV, BioEdit or other sequence editing programs. Compare your electropherogram with GenBank sequence and fill your gaps. Sometimes more than one peak place in same positition or sequencer read different nucleotide. Then you can resubmitt your 16S rRNA sequence to GenBank. You should check every nucleotide on sequence carefully.
Good luck.
Dear Dr/ Priti, I make blast to your sequence through NCBI-BLAST, link: https://blast.ncbi.nlm.nih.gov/Blast.cgi and I found that the identity is 96%, and query cover is 100% with Nostoc elgonense. It is not bad but it requires processing of your sequence after alignment using either BIOEDIT or MEGA5 programs. Further, you can submit your processed sequence through GenBank Submission tools using the following link http://www.ncbi.nlm.nih.gov/genbank/submit/ to acquire the accession number. GOOD LUCK
Hi Priti
I also got same issue from ncbi
Can you plz tell me how you rectify this problem.
Thanku.
Hi Adarsh
I have aligned the sequence again using MEGA5 Program and then submitted in NCBI and the problem was rectified.
Best Wishes
Priti
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