I need to find out the occurrence of specific sequences across the genome in both strands. I'm able to retrieve the FASTA sequence of the +ve strand from the NCBI reference genome.
How to get the -ve strand sequence of the Human Genome in FASTA format in the reverse direction?
I found a way to search.. If anyone comes through this question can follow ->
Make the Reverse complement of the query and search in the positive strand itself and once you get the hits, convert it back to the reverse complement to have the result in -ve strand.
Based on the post just above, the main question is technically not correct. Negative strand would just be the complement of positive. However, if you are considering the frame and direction, only then you can do it reverse complement.
Further, if the search would be query based, you don't have to do anything. The homology search tools like blast can give the strand information about where the hit is found. One do not have to do reverse complement of reverse complement.
@Abhijeet First of all, Thanks for the inputs and for your time.
Yes, I'm considering the direction for the same :)
My need was to find the unknown short sequences in the antisense strand in the reverse direction to coding sequences. In brief, I have short sequences in both ends with N number of unknown nucleotides in between.
The query is like this "sequence.......n.....N.....n....sequence"
Python Run with the database and query will help in identifying the same. To have the database of the negative strand in the other direction, I asked the question. However, since the -ve strand is complementary, I followed the above-mentioned method and succeeded, hence shared :)
Blast I can follow once I get these results, but not for finding unknown sequences :)
Thank you once again for your valuable input.
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