Hi everyone!
I found a gene from amino acid sequence by perfomed blast on NCBI. You may know the find-a-gene project by pevsner (http://www.bioinfbook.org/wiley/chapter5/Webdocument_5-16_findagene_globin.htm). I mean, I wanna tag the gene. Is there a way to submit NCBI? Anyone has any idea? Pls help me guys:))
So you want to add an annotation to a genbank entry which you didn't submit yourself, because you found a putative gene based only on blast as evidence?
Short answer, you cannot and you should not. Longer answer is here: https://www.ncbi.nlm.nih.gov/books/NBK53704/#gbankquickstart.although_i_m_not_listed
Blasting is not enough evidence (you need experimental evidence), you cannot derive sufficiently exact gene models from just blasting. If you want to submit something yourself, you could determine the transcript sequence by doing RACE-PCR on the target organism and submit the consensus sequence yourself to Genbank or attempt to submit derived gene models (mapping consensus to genome using e.g. exonerate) as annotation to TPA.
Sure blasting is not enough at all. I can explain whats the point, I'm interested to hear your advances. with a protein performed tblastn on est databse in one organism. I figured out that the orgaism has the protein. after this, blastx performed with accesion number of organism which taken from tblastn search. Results shows that the protein encoding gene is undetermined. This way is not enough to determine the gene on the organism?
It might be ok for your own use based on closely related species, even then your should use exonerate protein2genome to get a half-way ok coding sequence annotation. Noticed you are talking ESTs, ESTs are expressed sequences by definition, so you might want to add a gene name or function description to the entry?
You could contact the original submitter, that's the only way I could think of in addition.
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Hi welcome to biostars,
Please make sure your question is precisely stated and that you did your homework. How can I submit NCBI doesn't make sense. Please provide the necessary context or the question will be closed.
Is it good now?
What do you mean by "I wanna tag the gene"? Also, you didn't do an extensive search otherwise you would have found: The Genbank submission handbook.
the link is not my work, I put as an example. This project was my term homework and I have extensive search to sumbit NCBI. Thank you for your advance...
So you mean you searched "NCBI" and meant "Genbank"? You have not searched using google, I know that because: https://www.google.no/search?q=submit+ncbi shows the answers to your question as the top hit.
I searched on GenBank how to submit before. but needs more searches than blast as you told me. So wanted ask here. My lecturer said we can submit so I try to find it is whether possible.
Maybe you should walk through the documentation with your lecturer. Either your lecturer or 's lab has submitted the original genbank entry or your lecturer is trying to confuse you ;) May I suggest you to reveal which entry we are talking about to help my confusion and which gene you found?
the gene that encodes N-cadherin in axolotl. yes my purpose is to add a gene name
you mean https://www.ncbi.nlm.nih.gov/nucest/JK977486.1?report=genbank (longest sequence and best and longest blastx hit to N-cadherin, but not annotated as such)
or https://www.ncbi.nlm.nih.gov/nucest/50994465?report=genbank
As you can see, N-cadherin is already annotated to one of those EST's and there are in total two EST's as you can see from this query: https://www.ncbi.nlm.nih.gov/nucest/?term=n-cadherin+AND+axolotl+%5Borganism%5D
If you or your supervisor might have any more questions about the EST's annotation, e.g. why the best and longest hit was not annotated as N-cad while two shorter ones were, then you might read the paper and contact the submitters.
Btw, we could have gotten there immediately had you given me all the details.
Thank you so much Sir. I will share these information with my lecturer
I got the query and performed blasx with this. identity is %24 so all gene sequence have not been described yet