Hello everyone..
I am working on the role of transcription factors in abiotic stress tolerance in plants. For this, we have found a new gene (which is not available on NCBI/Genbank) from the sequencing of our plant's genome and done in-silico and in-vitro works with it. I want to know we can I publish these data without submitting the gene to any repository or is it compulsory to first assign an accession number and the proceed for publication?
Also, you guys please let me help to know that can we deposit the new 3-D model of protein in Protin Data Bank (PDB) without depositing the protein sequence in NCBI?
If you could show some special functionality of your gene, you could try to cowork with any company and probably patent your gene/functionality first. If you want to publish it, you have to show everything of it, the more, the better.
I have uploaded a Word file with a lot of examples of single biomarkers, we have detected and published. All publications could be found in ResearchGate, links are included.
Joachim R. Grün , Thank you sir. Now I want to know that, is it alright to submit 3-D model of our protein in PMDB (by selecting ''There is NO NR identifier for this protein'') without submitting the gene/protein sequence in Genbank?
PDB is a curated database, integrated with other bioinformatics data resources in order to make the available primary and derived data relevant to the molecule accessible to the scientific community.
Each protein entry in the database is curated with the data on 3D view, annotations, experiment, sequence, genome and versions beside the structure summary. Hence, each PDB record is integrated with the records relative to these data from the other relevant databases and so you find that the gene ID from NCBI is also presented in each PDB record.
Wonder why would you want to publish a protein 3D structure without presenting or depositing the gene sequence. The gene sequence/ primary sequence of a protein dictates the primary structure of a protein and has a significant role on the tertiary structure of the protein too. Unless you provide the primary sequence along with the 3D structure data, the information is incomplete for anybody who wants to study the structure and function of your protein.
Sorry, but I cannot help you with this part of your question. I hope someone else could do.
For NCBI submission, you can actually submit you sequences, get accession number for them and ask NCBI to hold the public access for your sequence fo certain amount of times after submission (i.e. one year or two).
That way, you can get accession number for your nucleotide and th e amino acid sequences. Moreover, you can get accession number for publication purposes.
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