Sequence Analysis programs - (Aug/11/2008 )

Hello All,

I have recently done some sequencings to check if my construct is in frame with GFP and I am getting heck of trouble analysing it as I sequenced backwards.

I was wondering how you guys check your sequencing results and if there is any program to make this task simple..

Thanks in advance.

I would suggest the Vector NTI suite from Invitrogen for sequence analysis since it has a lot of options including the reverse selection (for your case) to analyse sequences. For academic users the license is available free of charge. For very quick analysis the Expasy DNA to Protein translator ( http://www.expasy.ch/tools/dna.html ) is helpful. It translates your input sequence in all 6 frames (5'-3' Frame 1, 2 & 3 and the same for 3'-5' Frames). You should be able to judge immediately by looking into the 3'5' Frame (1, 2 & 3) whether your sequence is in frame with GFP or not. This is not recommended if you are looking for mutations.

Use one of the EMBOSS servers available around the internet (there's one here, a list of others is here). Use revseq to reverse your sequence, then translate it using transeq.