I got 97% matching in alignment for two genes " SUl-1 & blaCTX-M-15" isolated from Klebsiella pneumoniae ssp pneumoniae, so is it possible to get publish in gene bank database?
Then I submitted 2 gene sequences to NCBI gene bank and I got mail from them include these inquiries "If a sequence was obtained from a cultured isolate, then a strain name is required. A strain name is an alphanumeric identifier that may be designated in any manner, for example, it may be based on the name of an individual or locality. As an example, for Escherichia coli K12, "K12" is the strain name/identifier.
[2] We have noticed that some or all of the sequences contain reading frame shifts (insertions/deletions based on BLAST similarity search results and/or an alignment). This generally indicates there may be errors in the nucleotide sequence. "
What do they mean in frame shift deleted and I can identify the strain of the Microorganism Can anybody can help me?
These are semi automated answers from NCBI, so some may apply and some may not. But you won't be ale to submit until resolved.
As question [1] indicates, were your samples from a purchased or donated bacteria? or was it taken from a patient? If it is a clinical sample, you are not required to put the strain, but you may want to put it, just look at the best hits from your BLAST query. If you got it elsewhere, then the provider should have that information. If you don't know, you can put "Unknown".
Question [2] means they aligned the sequences to known genes in GenBank, and found that the sequences as they are would give a nonsense protein translation. Two common problems for this is that the sequence you're submitting is not starting at the canonical ATG, but starts at some internal point. You just have to specify which position of the gene your sequence begins. Another problem may be if your sequence contains more than one coding region (exons), and that in this particular organism and gene, and that they're not in sync, that is, between them there is a number of bases that is not a multiple of 3 (codons). That would make a "frame shift" since when translating the sequence, the aminoacids that would be decoded would be shifted by one (or two) bases, giving a nonsensical sequence with many stop codons. Usually this is fixed by specifying the CDS features, which are just descriptions on where a coding sequence begins and where it ends (they may even be overlapped), and then it doesn't matter if between them there is a nonsensical sequence that may or may not be a multiple of 3.
Having a point mutation (one base) which is a deletion or an insertion within a coding sequence of a viable organism is very, very rare, so usually they recommend to check your sequence. If a base was unreadable, how did you write it? if you used a "-" symbol, that means a deletion, but it is not what you want. I've seen people put an "N" instead, but I don't think that is correct since it is the IUPAC ambiguity meaning "any base". You could split your original sequence as two partial ones, leaving the trouble base or trouble sequence out altogether, and only submit the sequence before and the sequence after your problem sequence.
I found this web page useful, better than the obscure NCBI help pages. http://peter.unmack.net/molecular/data.sub/data.deposition.instructions.html
Hope this helps.
Good luck!
These are semi automated answers from NCBI, so some may apply and some may not. But you won't be ale to submit until resolved.
As question [1] indicates, were your samples from a purchased or donated bacteria? or was it taken from a patient? If it is a clinical sample, you are not required to put the strain, but you may want to put it, just look at the best hits from your BLAST query. If you got it elsewhere, then the provider should have that information. If you don't know, you can put "Unknown".
Question [2] means they aligned the sequences to known genes in GenBank, and found that the sequences as they are would give a nonsense protein translation. Two common problems for this is that the sequence you're submitting is not starting at the canonical ATG, but starts at some internal point. You just have to specify which position of the gene your sequence begins. Another problem may be if your sequence contains more than one coding region (exons), and that in this particular organism and gene, and that they're not in sync, that is, between them there is a number of bases that is not a multiple of 3 (codons). That would make a "frame shift" since when translating the sequence, the aminoacids that would be decoded would be shifted by one (or two) bases, giving a nonsensical sequence with many stop codons. Usually this is fixed by specifying the CDS features, which are just descriptions on where a coding sequence begins and where it ends (they may even be overlapped), and then it doesn't matter if between them there is a nonsensical sequence that may or may not be a multiple of 3.
Having a point mutation (one base) which is a deletion or an insertion within a coding sequence of a viable organism is very, very rare, so usually they recommend to check your sequence. If a base was unreadable, how did you write it? if you used a "-" symbol, that means a deletion, but it is not what you want. I've seen people put an "N" instead, but I don't think that is correct since it is the IUPAC ambiguity meaning "any base". You could split your original sequence as two partial ones, leaving the trouble base or trouble sequence out altogether, and only submit the sequence before and the sequence after your problem sequence.
I found this web page useful, better than the obscure NCBI help pages. http://peter.unmack.net/molecular/data.sub/data.deposition.instructions.html
Hope this helps.
Good luck!
Dear Christopher E Ormsby,
Many thanks for your valuable answer. Really it was confused about the strain of the microorganism, It become clear now. I have mutant genes sequences since I got 97% in BLAST alignment , I will send them the original file from sequencer source.
Are you certain that your genes are truly mutant? Before you make a claim that your genes are mutant you really need to be sure your sequencing was correct and is repeatable. A single sequence run is not sufficiently accurate to make this judgement.
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