Undergraduate Abhi Aggarwal has uploaded an elegant little program (.exe) that automagically translates and aligns forward and reverse sequence files!
To learn more about this program, read his article here:
Graphical User Interface. Photo of the main screen of the program. a) To translate a forward sequence read, this checkbox must be ticked to activate the drop box for the forward sequence. b) If translating a reverse sequence read, then this checkbox must be ticked to activate its respective drop box. Both checkboxes must be ticked to translate and assemble a forward and reverse sequence read. c) Once sequence reads have been dropped in or copy/pasted, user can proceed to translation and assembly algorithm by clicking the translate button.
Example of the frames window using a sample forward and reverse sequence reads. a) The forward sequence frame containing the largest open reading frame (ORF) is bolded. b) The reverse sequence frame containing the largest ORF is bolded. c) The size of the maximum overlap of amino acids between two frames is indicated for user’s discretion. d) The user can view the sequence frames in protein sequence or nucleotide sequence by choosing the appropriate button. e) Clicking this button will save all individual frames in the program’s memory, and allow for a side-by-side comparison with other sequencing frames.