Question: How to understand which DNA strand is (5' to 3' ot 3' to 5') in the result of blast ?
0
gravatar for arronar
5.8 years ago by
arronar200
Austria
arronar200 wrote:

Hi!

if a have such a result from a blast run, how can i understand if its in the 5' or 3' side of the DNA or protein strand ?

> gnl|SRA|SRR456295.4505.2 FIHSSUW02H237H.2 length=250
Length=250

 Score =   129 bits (324),  Expect = 1e-33, Method: Composition-based stats.
 Identities = 61/78 (78%), Positives = 68/78 (87%), Gaps = 0/78 (0%)
 Frame = +1

Query  203  RRMTLLLGPPGSGKTTLLLALAGRLNKDLKFSGQVTYNGHQMDEFVPQRTAAYISQHDLH  262
            R   L  GPP SGKTTLL+ALAG L K+LK SG+VTYNGH++ EFVP+RTAAYISQ+DLH
Sbjct  16   REWPLRPGPPSSGKTTLLMALAGTLAKELKSSGKVTYNGHELHEFVPERTAAYISQNDLH  195

Query  263  IGEMTVRETLAFSARCQG  280
            IGEMTVRETLAFSARCQG
Sbjct  196  IGEMTVRETLAFSARCQG  249

 

Thank you

blast sequence • 1.2k views
ADD COMMENTlink modified 5.8 years ago by Devon Ryan94k • written 5.8 years ago by arronar200

What are the possible values for Frame? +1,2,3 -1,2,3? If yes, then from that..

ADD REPLYlink written 5.8 years ago by 5heikki8.6k

There are some hits that have Frame +1 , others Frame +2 , or -2 , -1 and so on. How can i conclude something from this ? I thing that Frame refers on the triplet of codons used to align the sequence. 

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by arronar200

When I answered below, I had missed that you were using blastx. I updated my answer to answer what I think it is that you actually want to know. Yes, the possible frames are +1, +2, +3, -1, -2, and -3. If the frame is a positive number, then the aligned protein sequence arose from the DNA sequence you uploaded with a possible offset. If the frame is negative, then the aligned protein arose from the reverse complement of the sequence you uploaded (again, with a possible offset). Have a look at the wikipedia article on reading frames if you're not familiar with them.

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by Devon Ryan94k
3
gravatar for Devon Ryan
5.8 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

5' and 3' have no meaning when referring to amino acids. I assume that you mean N- and C- terminal. Since there's no concept of "reverse-complement" of a protein sequence, the sequences will always be N- terminal to C- terminal.

Edit: I missed that you were using blastx. Note that the frame is +1, so this protein alignment is made from the +1 frame of the sequence you used as the query. If you had uploaded the reverse complement of the sequence, then the frame would have been -1.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Devon Ryan94k
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