You can use the translate tool from the Expasy web serve (http://web.expasy.org/translate/)

1. paste your sequence in the big box

2. select your genetic code according to the animal model that you use

3. Output format:

- include nucleotide sequences if you want to place your STAR and STOP codons

4. translate your sequence.

You will get 6 different translations based on the direction and the first nucleotide readed.

In your results for translation you should choose one of the reading frames and select the STAR codon (Met). If your sequence is 700 bp you will get a protein about 230 aa

Afterwards you can check the translation by BLAST submission on ExPASy/SIB of your result. You should obtain the best hit with Cytochrome oxidase

There are softwares which can do the work for you. It does its work by extracting ORFs along the sequence. These ORFs correspond to different genes along your sequence. So a sequence may contain more than 1 gene. May I ask what sequence are you trying to submit to genbank? How many base pairs does it have? from what organism? cheers.

Cytochrome oxidase subunit I, about 700 base pairs,

You can use the translate tool from the Expasy web serve (http://web.expasy.org/translate/)

1. paste your sequence in the big box

2. select your genetic code according to the animal model that you use

3. Output format:

- include nucleotide sequences if you want to place your STAR and STOP codons

4. translate your sequence.

You will get 6 different translations based on the direction and the first nucleotide readed.

In your results for translation you should choose one of the reading frames and select the STAR codon (Met). If your sequence is 700 bp you will get a protein about 230 aa

Afterwards you can check the translation by BLAST submission on ExPASy/SIB of your result. You should obtain the best hit with Cytochrome oxidase

Yeah, you can do with Mega or Bioedit software (Hope you are familiar with this software).

But before doing so please select the suitable codon table and codon start site. (This option is available in "data" menu).

You can use online software CLCM workbench, which help you to sort out your problem very easily.

Hi, cytochrome oxidase subunit 1 is encoded by the mitochondria genome, so make sure that you are using the correct genetic code for translation (the mitochondrial one...).

Please be careful. You cannot - scientifically correcty - simply replace codons by others, be they stop codons or not. The only way to have an error-free sequence is to sequence, until ambiguities are solved.

Unfortunately, there is no other way to be scientifically and ethically correct.

Cheer up - Johannes.

Ditto to Johannes' answer. Double and triple check all your *original* data and edit if appropriate.

Johannes is absolutely correct. If you are "removing" stop codons, you DO NOT have the cDNA - you've sequenced something else.

You have problem in sequence editing.. see the raw data carefully. there may be very small peak which is being missed or due to bad quality raw data you are getting extra sequence.. I would not suggest you to go for any other method.. I am saying it by my own experience..

while making contig take a reference sequence of the same gene from the same organism that will help you to find out where you are wrong..

SeqScape software by ABI will be the most usefull.. or any software with which you can use reference sequence while contigue formation..

I am agree with Alejandro Romero

First, You should check the quality of the electroferograms using Bioedit (it's a free software) , and you may find if the stop condons are caused by a lecture error made by the equipement. In that case, you can correct the base manually and use the translate tool in order to check foros the presence of the stop codon.

I am agree with Johannes Wöstemeyer.

Please re check your sequencing results and use bioedit software for correction and also match with original sequence of gene of interest.

Johannes has made a very valid point. The sequence, including the stop codon, may be the correct one. There are many instances of mRNA editing & translational frameshifting which allow the production of the correct protein from a seemingly aberant transcript. Groups investigating these methods of regulation have problemts identifying them because people 'correct' their sequences before submitting them the GenBank!

I also agree with Johannes. On the other hand, not always can we return to the lab and (re)-sequence a gene. In such case, I'd suggest to try re-prediction of the gene in the sequence that you have. Step-by step it looks like this (for eukaryotic genes):

1. go to the gene prediction tool called Augustus (http://bioinf.uni-greifswald.de/augustus/submission/). It has a nice web interface, so you don't need to install it.

2. take the sequence of the gene in question +/- 1kb or more, depending on the species (characteristic lengths of intergenic regions) and the supposed length of the gene.

3. Put this sequence into the submission field.

4. Check if Augustus is already trained for your species (field "organism"). If not, select the closest relative available in the list. If there are several, try some of them (or all, to be on teh safe side).

5. Press "run Augustus".

6. On the result page, you will see the gene predictions for all possible transcripts (i.e., if there can be alternative splicing, the corresponding resulting transcripts will be shown).

If you have used several genomes, you can compare the results. In some cases the predictions made even for the "correct" genome are strange and not optimal (for the simple reason that some (rare) genes may have non-typical GC (and other) content and do not obey the genome "rules"). So if the re-prediction still does not give you the expected result (in other words, if the non-wanted stop codon is still there) you can try to predcit the gene with using the training for some closely related genome (select from the field "organism").

Please don't forget that all described above will give you only a hint, an idea of the possible correct gene borders. It is necessary to check its correctness with all available experimental methods. Even if you cannot re-sequence, there's still plenty of ways: does the mass fit to the MS data (if you have them)? Check the length with nothern blot; if you already know the length, just have a look if it still fits to your prediction. and so on.

Good luck!

Hi all, I really believe that the problem comes from not using the correct genetic code. as I pointed out earlier cytochrome oxidase subunit 1 is encoded by the mitochondrial genome, and therefore the mitochondrial genetic code must be used for correct translation.

If one tries to translate this gene or part of it using the standard genetic code, then one will see stop codons...

There is no need of fancy software to do this. The tool called 'translate' found on expasy allows to choose which genetic code to use for translation of a given nucleotide sequence.

I think Johannes is right. Firstly, you have to check if the stop codon was the real one in your sequence? that means you have to resequence the sequence you have sequence, if it is so, you have to submit it to GenBank. If it was created by error in sequencing, then you submit the correct one.

I agree with all that has been said here. Additionally - are you sure your gene prediction has not predicted pseudogenes? Those frameshifts may actually be very real and not just sequencing artifact. You could always design some primers flanking the region you are having troubles with and sequence the region to check, if you do not want to re-sequence the whole genome/larger fragment

I want to translate my 700 number gene data. How can i do together with error free stop codon? Please help

Which method of sequencing was used?

Do you have a unidirectional or bidirectional results?

If it was Sanger's; to what extent your fragments/ genes are conserved?

While agreeing with Wostemeyer, I can still offer some little help.

https://www.researchgate.net/post/How_to_remove_stop_codons_from_a_gene_sequence