DotKnot issues

[lstbl]

Hi everyone,

I have been trying to find a software package that will be good for RNA pseudoknot prediction. I want to use these predictions as an independent variable in a multiple linear regression to try and help predict the patterns of differential expression I see in an RNA-seq dataset.

I came across the program dotknot (a nice python program that uses the Vienna RNA program). It uses a modified version of the RNAfold program with a lower threshold value to predict pseudoknots. (http://dotknot.csse.uwa.edu.au/DotKnot_Manual.pdf)

I'm having trouble making the file for the program. I previously installed Vienna on my machine, but that version won't work for the DotKnot implementation. The error I get when making the file is:

/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in lib
make[2]: Nothing to be done for `all'.
Making all in Progs
gcc  -g -O2   -o RNAfold RNAfold.o ../lib/libRNA.a -lm 
Undefined symbols for architecture x86_64:
  "_LoopEnergy", referenced from:
      _fill_arrays in libRNA.a(libRNA_a-fold.o)
      _backtrack in libRNA.a(libRNA_a-fold.o)
      _circfold in libRNA.a(libRNA_a-fold.o)
      _stack_energy in libRNA.a(libRNA_a-fold.o)
      _energy_of_circ_struct in libRNA.a(libRNA_a-fold.o)
      _loop_energy in libRNA.a(libRNA_a-fold.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [RNAfold] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

any help would be very much appreciated!!!!

[lstbl]

Shamelessly bumping my own thread to prevent it from falling into obscurity.

I tried emailing the author of the program. Maybe she'll have a solution. Hopefully she'll have time to get back to me.

Alternatively, if anyone has any used any other method of predicting pseudoknot structures, I'd be grateful if you could share. I've exhausted my ability to find things on google/pubmed.

Thanks!