How to understand which DNA strand is (5' to 3' ot 3' to 5') in the result of blast ?
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
1 answer
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.
• 0 views
•
link
written
by
Devon Ryan
Log in to answer this question.
More posts like this
What are the possible values for Frame? +1,2,3 -1,2,3? If yes, then from that..
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.
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.