Question: How to understand which DNA strand is (5' to 3' ot 3' to 5') in the result of blast ?
0
gravatar for arronar
6.3 years ago by
arronar240
Austria
arronar240 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 • 1.3k views
ADD COMMENTlink modified 6.3 years ago by Devon Ryan96k • written 6.3 years ago by arronar240

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

ADD REPLYlink written 6.3 years ago by 5heikki9.0k

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 6.3 years ago • written 6.3 years ago by arronar240

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 6.3 years ago • written 6.3 years ago by Devon Ryan96k
3
gravatar for Devon Ryan
6.3 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k 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 6.3 years ago • written 6.3 years ago by Devon Ryan96k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1290 users visited in the last hour