Blastn(Strand= Plus/Minus and Plus/Plus) explication

Question

[midox]

Hello,

I posted my problem in another site but I have no answer. Maybe you can help me with my problem

I used Blastn to align reads with contigs. In the final report I have an alignments Strand (Plus / Plus) and Strand (Plus / Minus). "Minus" is the reverse complement or reverse of my contig? I know Blastn aligns both ways but do I have to consider the Strand (Plus / Minus)?

My goal is to find the parts alignment read-contigs. But in the case (Plus / Minus), is that this alignment is valid?

Thanks for your answer

Answer 1

[GenoMax]

Short answer is yes. If the alignments were not valid then blast would not have included them in the report. If you don't want to see hits on the complementary strand then you can turn them off.

-strand <String, `both'>, `minus', `plus'>
  Query strand(s) to search against database/subject
  Default = `both'

[midox]

If the "minus" it is reverse complement of to my contig, why do we find several contigs (Plus and Minus (reverse complement)) aligns with the only one reads?
Is it logical?

thanks

[GenoMax]

Since we can't see your data/results I can't comment if the result you are alluding to is logical. If the alignment was correct (within the parameters of blast that you used) then it is included in the results.

[midox]

I understand you.

generally, if there are for example two contigs: Contig A and Contig B (the first is "Plus" and the second "Minus") that align with a read in different places(for example).

are we can accept alignment of this two contigs? although the contig B it's the reverse complement (Minus) which is aligned with the read.

[GenoMax]

If I understand the drift of your question (based on past threads/discussions) ...

If contig A and contig B do not directly overlap then based on the blast result you only have evidence that they are on the same fragment of DNA and a certain distance separates them (based on where the blast hits end for the two).

Answer 2

[midox]

Hello, what's complexity of Blast if i use the Plus/Plus and Plus/Minis Option??

Thanks

[GenoMax]

Not sure what you are asking exactly. Can you add some additional detail?

[midox]

I'm talking about the complexity !! For example: for an alignment the complexity is O(mn) with m and n the length of the two sequences. but here there are two alignments Plus/Plus and Plus/Minus. it is the same complexity or O(mn+mrn) with rn the complement-reverse of the second sequence. Did you understand me? thanks