DNA alignment strand
I used Blastn to align reads my DNA sequence. In the final report I have an alignments! Strand (Plus / Plus) and Strand (Plus / Minus). But, there was 1 sequence with (Plus / Minus) result while the another 5 sequence was (plus/plus), is the (plus/minus) strand was valid alignment?
This is the sequence:
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Ram
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Farra Sho •
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Farra Sho •
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I guess it depends on the source of your DNA sequence, how you isolated it, and the goal of your alignment.
For example, if I was inserting a gene into a plasmid and sequenced the ligation product using a forward primer, I may expect the plus alignment to my reference, but if I got a minus alignment, that may mean the gene was inserted in wrong direction.