Hello everybody,
First of all I did my homework and before ask, I looked for this question with google and in this forum but I didn't get the information that I want.
If I did wrong, I'm sorry.
My question is about appropriate use of database effective length option performing BLAST.
I have a scaffold of my specie of interest and I have to find whether a specific gene from another related specie is in this scaffold or not. The fact is that my scaffold has a lot of 'N' in such way that the 41.3% of it are 'N'.
I was wondering if it would be appropriate "tell" BLAST database effective length is a 41.3% smaller so I would get more fitted expected values.
For me it makes sense, but I am totally novice in these fields.
Thank you in advance!
First of all I did my homework and before ask, I looked for this question with google and in this forum but I didn't get the information that I want.
If I did wrong, I'm sorry.
My question is about appropriate use of database effective length option performing BLAST.
I have a scaffold of my specie of interest and I have to find whether a specific gene from another related specie is in this scaffold or not. The fact is that my scaffold has a lot of 'N' in such way that the 41.3% of it are 'N'.
I was wondering if it would be appropriate "tell" BLAST database effective length is a 41.3% smaller so I would get more fitted expected values.
For me it makes sense, but I am totally novice in these fields.
Thank you in advance!
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