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Are there tools for finding ORF for multiple sequences

Hello guys, I have a several thousands of de novo assembled sequences form RNA-seq, some of them are annotated and some them are not. If I wanna predict their ORF for checking out for how many of them have complete ORF and how many does not?And where is the Start codon and where is the Stop codon?How i am gonna do that? Is there any tools? Thanks in advance.

finding orf

Hi Kurban, please don't make revisions that in effect turn the question into a completely different one. Please open a new question after carefully searching for existing questions.

1 answer

Percentage is the fraction * 100%

How is this related to question at all?

This was an answer to another question, I don't know why it ended up here now?

Before modification the question was:

How to calculate the percentage of genes (unigenes/transcripts) enriched to each

I find this quite often! Users ask questions, once you give them the answer, instead of proposing another question, they change the original one! It makes no sense and at the end you completely miss the information.

Unfortunately, we don't have revisions any more. I think that having revision tracking in place would help.

I'm afraid, revision might help but it fixes the effect not the cause! One should keep in mind even by getting the answer he looked for, he should leave the question. The question is as IMPORTANT as the answer.

I agree, the question and answer together form the added value, if and only if these two are related. However by using the revision system, a moderator could restore the content to the initial state. Another helpful mechanism would be to be able to lock posts for editing.

I never realized that this would actually happen.

Normally it would make no sense for someone to do that. But now that I thought about it here are possible reasons:

  • New users can only create two questions per 6 hours, so it is possible that someone thinks this is a way to ask a new question right away. This falls into that "unintended consequences" category.
  • Perhaps the users realizes later that their question is really about something else want to correct the original question.

The solutions are not easy to either, we do want to allow people to fix up titles and typos, pushing a new version for each of these is somewhat of an overkill. So is maintaining the infrastructure to view, display and revert the changes. We have to see how this evolves.

IMHO, one solution could be to lock the editing option once an answer was given (before that he may change it as much as he wants!), the one who is asking still can add comments and replies, the new comments, ideas and its answers will flow in harmony afterwards!

Making questions locked on the first answer might be overly strict, because questions could get clarified or improved in the light of a first answer, e.g. if op sees misunderstanding or is asked for clarification, even after an answer has been accepted. To not be able to edit own questions at all would maybe feel scary also. A versioning system for questions and answers -like on SE- could be part of the solution, it was there in a previous version, but somehow was removed in between.

I remember a case where there was an interesting question comparing the RNA seq tools Kallisto and Salmon and suddenly the content of the question disappeared, without further explanation. Maybe op made a mistake or whatever, it still would have been worth discussing the results.

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