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Question

[ashamscsoft]

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?

[benaneely]

Within emboss, are you using transeq or getorf?

[ashamscsoft]

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

Answer 1

[Devon Ryan]

Take the longest single stretch of highlighted sequence.

[ashamscsoft]

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

[Devon Ryan]

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

[ashamscsoft]

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.

[Devon Ryan]

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.

Answer 2

[EVR]

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.

[ashamscsoft]

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