Frame-Pro Files

Sample code for Frame-Pro

There are four python files:
dagcon_io.py is a simple implementation of input and output test file.
hmmdagcon_pacbio.py is main program including the viterbi algorithm.
aligngraph.py is modified DAG-Con aligngraph package
aminoacid.py is a package deal with the aminoacid translation.

To start a simple task, you need following input.
1 A fasta file with backbone sequence.
2 A m5 file from BLASR. Noticed we used backbone sequence as query seqquence to align other short sequence. In practical, this will make all alignment have same direction to backbone sequence. Since we revert the query and target, so when run BLASR we suggest to set -bestn 200.
3 A hmm file from Pfam or in Pfam format.

As you know, we are still working hard to improve the efficiency and packege the whole pragram. So check the website later to see updated version.