I've added multiple reading frame translation and reverse complement translation along with control for the number of nucleotides per line.

http://nadv.herokuapp.com/

If you are looking for something that will translate your nucleotide sequence to Amino Acids after the stop codon and display it like your example then you can use this tool I just wrote today to give you a display like you are looking for. You can download the results to a text file and then add your annotations on top of the alignment. Let me know if you have any problems or if this is useful.

http://nadv.herokuapp.com/

Congratulations, Sean! You've done an excelent job! Many and many thanks!!! It will be very useful and I suppose not only for me (if you want some help to share the link just tell me!).

If you want to improve your tool, I suggest you follow the way that allow the user to choose the reading frame as well as the side numbers are displayed (as it changes according to the journal). It would be perfect if the background was white and without underline between amino acid codes.

Milena,

You can download the text file version that has no underlines - just spaces as long as your using a monospaced font. That way you can use a text editor or other tool to highlight the various parts of your sequence for annotation. I will consider adding other reading frame choices and letting a user choose the number of nucleotides per line.

I've added multiple reading frame translation and reverse complement translation along with control for the number of nucleotides per line.

http://nadv.herokuapp.com/

Milena and Sean,

While it is perfectly ok to work on a tool of your own, I am sure there are plenty of available programs for this kind of jobs, such as EMBOSS Sixpack: http://www.ebi.ac.uk/Tools/st/emboss_sixpack/ Just type "sixframe translation" or "ORF translation" into Google to find more.