I gave a code to a bacterial strain using asterisk but when I submitted its 16S RNA sequence to GenBank I get an error message saying that I have to change the code with alphanumeric one. I have submitted an article before to an international journal, so should I change the code and inform the journal about this change? or there is another solution. Thanks a lot.
Hi Dear
firstly submit your results to NCBI and after check you will get ans accession no.
BR
I think you have cultivated bacteria, or one strain, from a sample, and you are asking what 'system' you should use to name them (or it). You used a symbol (*), but then found you cannot use that symbol in a name provided for the GenBank record. If all that is correct, I can only tell you there is no convention, to my knowledge, that dictates how we name any culture in our own labs, just as there is no convention for the naming of probably anything in our own labs! However, 'simple makes sense'...
I first use, and encourage my students to use, their own initials. Then add a number which starts at 1, and increases from there. So, I've had in one project SD1 through SD672. I know where each culture comes from and how it grew because I recorded all those data; there's no need to have long descriptive culture names, such as 'SD276round*shiny_A'. I can write SD276 on a Petri dish, on a small tube, in GenBank, and the rest of the information is in a notebook, or spreadsheet, etc.
Now, I have cultivated microbes from many places, so I might instead use 'L1' through 'L30', where 'L' is Loihi. Or PH27A is culture 27A from Pearl and Hermes Atoll. 'LA' is Laysan. These labels are short and easy to write on Petri dishes or tubes. And GenBank will accept them, although that is not my motivation for short labels!
To recap, you can call your own cultures what you want to call them, but I'd suggest you stick to an alphanumeric system, as you suggested. Avoid symbols and long descriptions. As others have responded, too, a journal is unlikely to publish without a GenBank accession number for any sequence you report. You've found you can't get the accession number if you have an asterisk in the culture designation/code; change the culture designation, perhaps only by removing the asterisk, then complete the upload to GenBank, and update the culture designation code when you are revising your manuscript in response to reviewers' comments. A reviewer (or more) will probably notice you don't have the GenBank accession number, so you'll have to add that when revising. That is when you can edit the culture's name in your manuscript, too. There's no need to write to the editor at this point just to tell him/her this minor detail.
Thanks a lot Mr Stuart for your time and explanation. I had removed the asterisk and putted a number, and I submitted the sequences and get the accession numbers.... Thank you again.
Usually special characters like * are not recognized in the databases. Need not to worry change your strain code into alphanumeric. submit the sequences in GenBank, get accession number. After having accession number just inform your journal about the change and update them regarding the accession number.
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