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While writing my paper, I was unaware of the existence of a sequence and I named the sequence (say X). Later I found that the same sequence is already known with some other name (say Y). Currently if my paper is under review, then can I change to Y according to the literature and resend? Or is it okay to continue with the name X I sent?

Note that the novelty of the paper does not completely rely on the sequence used.

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    you will have a chance to correct this after the review. – louic Aug 28 '18 at 12:28
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    @wonderich Please do not answer in comments as it bypasses the stackexchange system. For your comment: Could you please provide an answer including the information as to why you think they should? – Dirk Aug 28 '18 at 18:18
  • What is "sequence" in this context? Something mathematical? – Peter Mortensen Aug 28 '18 at 18:23
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    @Peter: A sequence is something mathematical, yes -- en.wikipedia.org/wiki/Sequence -- and that is presumably what is meant in the context of this question. – Pete L. Clark Aug 28 '18 at 20:24
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From what you have written regarding the sequence name, it sounds like this it only a question of nomenclature and doesn't substantively affect either your results or the novelty of these results.

If this is indeed the case, then it can easily be amended at revision. Pretty much every meaningful peer review process on a significant article will end up requesting at least minor revisions, since reviewers will generally contribute useful perspective and few manuscripts are without at least some typos.

If there is a major impact (presumably on novelty), it is a whole different story. Depending on how large the impact, you might either still want to wait until revision (e.g., if it's going to replace a couple of paragraphs with a citation) or you might even want to withdraw and resubmit a new version of the manuscript (e.g., if it results in dropping an entire section). Even if you need to do something so extreme, however, I would not worry overmuch about consequences: any good editor will respect (and likely appreciate) such a decision.

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    Withdrawal is probably a last resort. It's certainly something you should discuss with the editor before doing. if the paper is just withdrawn, it's likely that the referees' work so far is wasted. On at least one occasion, I've received a revised version of the paper mid-way through reviewing it, along with a description of what had changed, which was very local in scope and didn't affect anything I'd already gone through. – David Richerby Aug 28 '18 at 17:43
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    +1 and I'll add that in the unlikely event the paper is accepted without review, you can write to the editor then and say you need to make this change. It sounds like the change is non-controversial (i.e. doesn't need to be peer reviewed), so you can even make the change during the production process. – Allure Aug 29 '18 at 0:04
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I agree with the other two answers (by Buffy and jakebeal), but I would also add another possibility that I've seen people make use of. First, note that I don't understand how important this change is, so I'm not necessarily saying you should use this approach — just that it's a possibility.

You can contact the editors even while the paper is out for review to mention that you'll need to make this change. From what you say, it sounds like they'll probably just tell you to wait until you get the paper back to do revisions. It's also possible that they'll forward that information to the reviewer, which may preempt an issue the reviewer planned to raise.

Again, I can't judge whether or not this is the right approach for you, but it has happened to me that the editors of a journal contacted me while I was reviewing a paper to pass along important information from the authors, and it helped with the process. In any case, you really should correct this at some point before publication, for the sake of academic integrity.

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Generally speaking the version submitted to a journal or conference is not the version published as it will go through review. However, the nature of the change can affect things. In the worst case, the paper has a predecessor that makes its publication moot, or even invalidates the conclusion. But in the usual case you can make such changes. However, the extent of the changes may make it necessary to have it reviewed again. That is easier for a journal to do than a conference, which has harder deadlines.

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The way to handle this is to add a note - either as a footnote or in the body of the text - indicating that the sequence has a different name elsewhere, and include appropriate reference in an updated bibliography. Of course this assumes the referee will not herself/himself point out that fact in the report.

At the time of resubmission (if some changes are required) or when you next contact the editorial office, indicate clearly for the benefit of the editor (and possibly also the referee) that you have added bibliographic entries and why, and that you have added some text (and indicate where) to clarify the issue.

A well written note explaining how this doesn't affect the novelty of your work should do it but, if the referee is unaware of the said reference and the paper is accepted without further review, the editor can always go back to the referee if she/he feels this compromises the integrity of the manuscript.

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