NMalign2

The program NMalign2 implements a simple dynamic algorithm to align the nucleosome profile of a query on the nucleosome profile of the reference according to the genome alignment of the query on the reference. The algorithm works chromosome-by-chromosome as follows:

• Assumption: two nucleosomes are said to be “unambiguously aligned” if the distance between their midpoints is lower than half of their average size.
• Initiation: find all unambiguously aligned nucleosomes along the chromosome.
• Recursion: between two consecutive unambiguously aligned nucleosomes
  • if there is no unaligned nucleosome in the interval, then go to the next unambiguously aligned nucleosome.
  • else:
    • Align nucleosomes by minimizing physical distance between aligned pairs.
    • The remaining nucleosome(s) are considered as insertion(s) (if they are reference nucleosomes) or deletion(s) (if they are query nucleosomes).
    • Go to the next unambiguously aligned nucleosome.

To run NMalign2, we need first to write a short configuration file that will tell the program where he can find the difference sources of information require to process the nucleosome alignment. We already put such a file into the folder S4:

$NMalign2 -c S4/NMalign.conf -o S4/NMalign

This can take some times, so be patient. In fact, NMalign is doing a bit more jobs than aligning the nucleosome profiles, increasing the computation time. This should be improved in the next release of NucleoMiner. As you can see, the program has created a new directory S4/NMalign into which one file per chromosome has been created. This .nal file is a binary file storing the result of the alignment and some other useful information that will help to speed up subsequent analyses.

In order to generate human readable version of these .nal files, we have to run again NMalign by using now the --print= flag as follows:

$NMalign2 -i S4/NMalign/ -o S4/NMalign/ -c S4/NMalign.conf --print