I have isolate the MtDNA from different Noctuidae moths. From the MtDNA i sequenced the COI gene (Cytochrome oxidase sub I). When i submit the sequence to NCBI,C they asked to submit the Coding region (CDS features). So i need to submit the CDS along with the sequence.
When I have had any doubt about what to submit. I have e-mailed them: [email protected]
They will guide you step-by-step. If not, you can just BLAST the nucleotide sequence to see which cDNA is your hit. If this moth had not a sequenced genome, you may be able to use a close organism (fly?)
Dear Siva,
You could start by entering your sequence into GENSCAN http://genes.mit.edu/GENSCAN.html - this is a great annotation tool.
"GENSCAN is a general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants"
"For each sequence, the program determines the most likely "parse" (gene structure) under a probabilistic model of the gene structural and compositional properties of the genomic DNA for the given organism. This set of exons/genes is then printed to an output file (the text output) together with the corresponding predicted peptide sequences"
Good luck!
Dear Rolando Garcia-Milian
Thanks for valuable information. I try work in this tool
with regards
Dear Siva,
Before you went for sequencing you must have used a primer which u used to amplify your gene of interest? did you design yr primer or you got information through literature survey because the primer alone as designed based on CDs? Secondly, its important you blast your sequence in BLAST, based on the maximum scores you attain as stated above, get that particular information i.e gene showing maximum score compared to your gene in which CDs information is given, then go for GENESCAN, which will show you starting sequences. Logically, based on the hit score, u can actually be able to locate you CDs. All the best.
Good number of the sequences are available in NCBI for Noctuidae moths cox I. You go for best match and pair wise alignments with BLAST. I think it is very easy.
Dear Siva.....
Translate you DNA sequence to protein and Do Blast and ClustalW,, choose maximum identify and ensure the outcome graphics u obtain consisting of amino acids has no stop codons, so within tht u got ur CDs
Hi
Simply go to the expasy translate tool, paste the DNA sequence and ask to translate. Select the sequence in the proper coding frame and blast it. once the selected frame gives the correct hits with complete coverage of full length gene sequence, just submit the same. if you have amplified the truncated portion of the gene, submit the truncated part of DNA sequence only that encodes the protein of interest in the proper reading frame.
Good luck
BASAVARAJ
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