I have 3 nt sequences a virus gene and am using Sequin to submit the sequences to the GenBank. I tried more than two online software or ORF finders to do the annotation before manual entering of the CDS into Sequin. I got different CDS by each program and thus felt confused. I used a gene finder and it looks I have two genes in each of the sequences. What is the best and correct program to annotate such sequences and what are the detailed steps I have to follow in order to successfully make the annotation?
Convert your annotation to agp format then submit it.
http://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/
Artur Burzynski: Many thanks for your valuable comments. I understood that any annotation software can be used and its feature and CDS will be accepted by for example GenBank. Assuming I already annotated my sequence and wanted to complete the GenBank submission; opened the Sequin tool, continue till annotation step, selected the target sequence and moved to coding region and transcript…CDS. My concern is here. When the coding region tab is selected I must select from 3 reading frames 1,2 or 3. How to select the correct for my CDS and how to proceed providing the CDS location particularly if I have two separate CDS in my sequence and when the obtained annotation contain the following records { 805, C(421..513, C(713.. >805), 618..689, 280..351,115..183,119..154}. Hope I clarified the issue.
Kashif Nawaz: I thank you for the suggestion. I may need some more details. How to convert the annotaion into AGP format?. Any online software?. And also, where and how to upload this AGP file within the annotation menu of Sequin.
In one possible way you can use fasta2agp.pl (not written by me) to convert your CDS fasta sequences to agp format. For the submission you can directly mail to NCBI ([email protected]). Hopefully they will assist you.
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