A couple of folks have pointed out deficiencies in the current version of CleaveLand2. One annoyance is the reliance of the target prediction script upon the SHRiMP program; the CleaveLand2 script 'axtell_targetfinder.pl' was built for version 1.X of SHRiMP but SHRiMP is now into version 2.x, which, among other changes, has messed with the command line switches used in 'axtell_targetfinder.pl'. Another issue is the very clumsy way some of the scripts handle file paths and naming, which causes failure of the process if a user does not have input files located in the working directory.
So ... I am working on a revised version of CleaveLand2 to fix these issues and hopefully improve performance. The major philosophical difference between CleaveLand2 and the CleaveLand 1 version that we published on is the use (in CleaveLand2) of extensive randomized target predictions to estimate an ad-hoc p-value. I really like this approach, but it is computationally expensive to get alignments of 1,000 random miRNA queries for each real miRNA query. In my revision, I may try and find a shortcut around this ....
So, anyway, for people who are waiting for me to fix these issues, please stay tuned. I'm on it. -- mike axtell
So ... I am working on a revised version of CleaveLand2 to fix these issues and hopefully improve performance. The major philosophical difference between CleaveLand2 and the CleaveLand 1 version that we published on is the use (in CleaveLand2) of extensive randomized target predictions to estimate an ad-hoc p-value. I really like this approach, but it is computationally expensive to get alignments of 1,000 random miRNA queries for each real miRNA query. In my revision, I may try and find a shortcut around this ....
So, anyway, for people who are waiting for me to fix these issues, please stay tuned. I'm on it. -- mike axtell