I have several sequences which I'm blasting against the nt database, and I wanted to know how to retrieve for each hit the intervals matched.
As far as I'm aware, the standard output only gives this interval both in the query and reference sequence for the largest continuous match.
What happens many times is that my query sequence has more than one continuous match, for which I will also would like to know the positions.
For example,take this as my query sequence with results for some organisms from the nt DB that matched at some positions:
M=match
-=Nothing aligns here
---MMMMMMM-------MMMMMMMMMMMM
In this case I will only get the interval positions for the second match, but since the first is also large I will want that.
I'm running these on my local computer with the standalone blast.
How can i make this happen?
The reason why I want to do this to see how much of my query sequences cover some organisms.
