Question about MiRanda output file - (Jul/26/2007 )

Hello

I have question about MiRanda. I am using Linux version.

I am using this software to prediction of potential micro RNA targets sites in human 3'UTR database from Ensemble (about 31000 sequences). When I get output file I see thousands of ,,No hits found above threshold'' and only
100-200 positive hits. My problem is to how can I get only positive hits from output file
because this file is too big to work with it? I can't find any command for this in
Miranda manual.

Best regards

-leblaszczyk-

Even you use the "-quiet" option, you still get "No hit ..." lines in the output file. A simple perl script can help get rid of those lines.

-pcrman-

THX for Your help:) It work:)

-leblaszczyk-

I have other question, about miranda settings. I use default setings:

Gap Open Penalty: -8.000000
Gap Extend: -2.000000
Score Threshold 80.000000
Energy Threshold -14.000000 kcal/mol
Scaling Parameter: 2.000000

I saw this settings in several publications but i don't have expirience in miranda. Do You think there are optimal settings? What can i change to get more specific results?

-leblaszczyk-