Question: Open Reading Frame
0
gravatar for ashamscsoft
4.5 years ago by
ashamscsoft20
ashamscsoft20 wrote:

My doubt is if we give our DNA sequence in Expasy or emboss translate it translates the sequence into 6 frames,highlighting some aminoacid sequence in each frames. Now my question is if we want to buid a protein structure using that sequences, we should take all the highlighted sequences in each frame and combine or we should take which frame is larger? Can anyone help me with this?

amino acid sequence • 1.0k views
ADD COMMENTlink modified 4.5 years ago by EVR570 • written 4.5 years ago by ashamscsoft20

Within emboss, are you using transeq or getorf?

ADD REPLYlink written 4.5 years ago by benaneely70

i'm using transeq for translation if i give translate sequence, it comes frame by frame only

ADD REPLYlink written 4.4 years ago by ashamscsoft20
1
gravatar for Devon Ryan
4.5 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

Take the longest single stretch of highlighted sequence.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Devon Ryan97k

Then what about the other sequences that are highlighted in other frames?

ADD REPLYlink written 4.4 years ago by ashamscsoft20

Normally they can be ignored. Sometimes those will end up being other proteins, often not.

ADD REPLYlink written 4.4 years ago by Devon Ryan97k

thank u and i have one more doubt can u help please? If i take mutated sequence of gene and i'm converting that sequence to protein structure. After converting to protein structure can i do docking with that structure.

ADD REPLYlink written 4.4 years ago by ashamscsoft20

Sure, though I'm not up on how good the protein folding algorithms are these days, so I can't say how reliable the results will be.

ADD REPLYlink written 4.4 years ago by Devon Ryan97k
0
gravatar for EVR
4.5 years ago by
EVR570
Earth
EVR570 wrote:

Hi,

Also check whether the largest amino acid sequence has BLASTp homology hit or any domain hit to be very confident that selected peptide is significant with hits. Also take a look at Transdecoder.

ADD COMMENTlink written 4.5 years ago by EVR570

Is there any reference for this, then what about the other sequences that are present in other frames? Kindly suggest if there is any reference please

ADD REPLYlink written 4.4 years ago by ashamscsoft20
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