When we submit the gene sequences to NCBI, the start codon and translation tables of sequences is also needed.
I think you need to first know what the partial gene sequence is ? This can be done based on similarity search of related sequence of same gene in same species or different species. As the gene sequence has proximal and distal end and if you have already confirmed that your partial sequence is from proximal end then you can start looking at many online software to find your start codon of your partial sequence.
First you need to confirm you DNA Sequence by similarity search using BLAST. After you confirm you gene. You can use the partial fragment in NCBI ORF finder or other related software like MEGA, etc. where you need to specify the codon table and you get the start codon of your partial gene fragment.
Try it..Good Luck.
Hi siva,
You just do a translate your DNA to protein using this tool link http://insilico.ehu.es/translate/
You will get results with 6 frames .
Choose the best one , with no internal frameshifts or stop codon,.
That frame would be the right form for submitting it to the NCBI.
Regards
Murugan N,
2010 Loyolite
Do a BLAST search on NCBI. That should give you an idea. However, complications will arise if you are looking at alternatively spliced transcripts. You may get multiple transcripts that encompass your sequence, yet start / end at different points.
Best,
How would you say that your sequence is partial? You can try your sequence with Genscan. It will show that whether your nucleotide sequence possess which type of exon i.e. complete exon, middle exon, terminal exon. If your sequence is middle or terminal exon it wont have start codon.
Thus you can identify the availability of start codon from your sequence.
You can choose the codon preferable table on the basis of source organism. You can find the codon table from the following link: http://www.kazusa.or.jp/codon/
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