Hi,
I have amplified a partial gene sequence of a bacteria with the help of degenerate primers and want to submit it to NCBI, but when I am doing CDS analysis in BLAST getting 74% similarity and there are 10 gaps (2%). Kindly help me how can I submit this sequence to NCBI. Is it alright to delete the gaps and submit your sequence?
Thanks in advance!
Abhijeet Singh
- submit different fragments separately, best option in your case
- you might also consider replacing gaps with Ns, but for that one must know what and how to do things. If there is any misunderstanding/error in your analysis, this method would not work. Most probably you have used Sanger sequencing and a lot of factor can influence the final sequence.
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Ahmed Mousbah
Hello
please read the following link
Gapped Format for Genome Submissions
https://www.ncbi.nlm.nih.gov/genbank/wgs_gapped/
Good Luck
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