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Inference of couplings in proteins and RNAs from sequence variation

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- - end_to_end.yml
  - main.yml
- .gitignore
- - potts3.a2m
- - DHFR.a2m
  - DHFR.png
- - RF00162.fasta
  - RF00162.png
- .gitignore
- export_couplings_json.m
- plot_coupling_scores.m
- read_params.m
- run_examples.m
- - arithmetic_ansi.h
  - arithmetic_sse_double.h
  - arithmetic_sse_float.h
  - inference.h
  - lbfgs.h
  - plm.h
  - twister.h
  - weights.h
- - lbfgs.c
  - twister.c
- inference.c
- main.c
- plm.c
- weights.c
- DHFR.couplings
- DHFR_weights_raw.txt
- protein.sh
LICENSE
makefile
README.md

// repository documentation

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# plmc
plmc infers [undirected graphical models](https://en.wikipedia.org/wiki/Markov_random_field) to describe coevolution and covariation in families of biological sequences. With a multiple sequence alignment as an input, plmc can quantify inferred coupling strengths between all pairs of positions (couplingsfile output) or infer a generative model of the sequences for predicting the effects of mutations or designing new sequences (paramfile output).

## Usage
      plmc [options] alignmentfile
      plmc -c couplingsfile alignmentfile
      plmc -o paramfile -c couplingsfile alignmentfile
      plmc [-h | --help]
      
    Required input:
      alignmentfile                    Multiple sequence alignment in FASTA format

Options, input:
      -w  --weights    weightsfile     Load sequence weights from file (one weight per line)

Options, output:
      -c  --couplings  couplingsfile   Save coupling scores to file (text)
      -o  --output     paramfile       Save estimated parameters to file (binary)
      --save-weights   weightsfile     Save sequence weights to file (text)

Options, alignment processing:
 -s --scale <value> Sequence weights: neighborhood weight [s > 0]
 -t --theta <value> Sequence weights: neighborhood divergence [0 < t < 1]

Options, Maximum a posteriori estimation (L-BFGS, default):
 -lh --lambdah <value> Set L2 lambda for fields (h_i)
 -le --lambdae <value> Set L2 lambda for couplings (e_ij)
 -lg --lambdag <value> Set group L1 lambda for couplings (e_ij)

Options, general:
 --fast Fast weights and stochastic gradient descent
 -a --alphabet alphabet Alternative alphabet (default 21: -ACDEFGHIKLMNPQRSTVWY)
 -f --focus identifier Select only uppercase, non-gapped sites from a focus sequence
 -g --gapignore Exclude first alphabet character from potential calculations
 -m --maxiter Maximum number of iterations
 -n --ncores [<number>|max] Maximum number of threads to use in OpenMP
 -h --help Usage

## Compilation
plmc requires no external libraries, but can optionally be accelerated with OpenMP for multicore parallelism.

**Multicore**. To compile with `gcc` and OpenMP:

make all-openmp

**Multicore, macOS**. To install OpenMP through homebrew and compile with `clang`:

brew install libomp
    make all-mac-openmp

**Single core, Linux**. To compile with `gcc`:

make all

**Single core, macOS**. To compile with `clang`:

make all-mac

**Single precision**. All of the above targets compile to double precision (64 bit), but reducing the precision to single (32 bit) increases speed and decreases memory requirements by approximately a factor of two. The fastest compile settings are then:

make all-openmp32

## Output

**Coupling scores**. The `couplingsfile` is a flat text file containing scores quantifying the inferred strength of the coupling between every pair of positions. It has 6 columns: `RES_I FOCUS_AI RES_J FOCUS_AJ 0 SCORE`, where `SCORE` is the coupling score between positions `RES_I` and `RES_J`, `FOCUS_AI` and `FOCUS_AJ` are the letters in the focus sequence (optional, `-` if no focus), `0` is a placeholder. The `SCORE` values are APC-corrected Frobenius norm scores, but alternative scores can be computed from the raw parameter values.

**Parameter estimates**. The optional `paramfile` specified with `-o`, will store all inferred model parameters in binary. These can get large, as for proteins the model explicitly parameterizes all possible pairs of amino acids at all possible pairs of postions, which is about 106-108 numbers for families of lengths ~70-700. The MATLAB script `scripts/read_params.m` unpacks this binary file into model parameters as well as associated metadata, such as inferred sequence weights.

**Sequence weights**. The optional `weightsfile` specified with `--save-weights` (and loaded with `-w`) is a flat text file containing one floating-point weight per line. Each sequence's weight is the inverse of the number of neighboring sequences with less than θ percent divergence.

## Examples
**Protein alignments**. The example directory includes an alignment of the protein [dihdyrofolate reductase](https://en.wikipedia.org/wiki/Dihydrofolate_reductase) (DHFR). To infer a model for this family, we can type the following in the base directory:

bin/plmc -o example/protein/DHFR.params -le 16.0 -lh 0.01 -m 100 -g -f DYR_ECOLI example/protein/DHFR.a2m
The numeric options set a strong L2 regularization for the couplings, λe = 16.0, a weak L2 regularization for the sites, λh = 0.01, and the maximum number of iterations at 100. The focus `-f` option tells plmc to only model columns that are upper-case in the E. coli sequence DYR_ECOLI (NOTE: for focus mode, the alignment should only contain columns that are coding in the focus sequence, otherwise the offsets for the output sequence will be incorrect.) The `-g` gap-ignoring option ignores gaps by modeling only the coding portions of each sequence. To read the binary paramfile `DHFR.eij` and visualize the couplings, we can type the following in MATLAB from the `scripts` directory:

params = read_params('../example/protein/DHFR.params');
    plot_coupling_scores(params)

This computes and plots the same (APC-corrected) coupling strengths that would be output to couplingfile, revealing many strongly coupled pairs of positions in the long-term evolution of DHFR:
<img src="example/protein/DHFR.png" width="500">

Each coupling strength summarizes a larger set of coupling parameters, since the model explicitly parameterizes each possible combination of amino acids at each pair of positions. To visualize these sequence-level parameters, we can use a JavaScript tool [EVzoom](https://github.com/debbiemarkslab/EVzoom) that is designed to visualize plmc models. For efficiency, we export only the strongly coupled pairs (culled by an EM-based outlier-detection method) in a lightweight JSON format with

export_couplings_json(read_params('../example/protein/DHFR.params'), '../example/protein/DHFR.json')

[EVzoom](https://github.com/debbiemarkslab/EVzoom) makes it possible to navigate the large number of sequence-level parameters present in undirected models of sequence families:
<img src="https://marks.hms.harvard.edu/evzoom/evzoom.gif" width="500">

**RNA alignments**. 
 An example RNA alignment is included for the [SAM riboswitch](https://en.wikipedia.org/wiki/SAM_riboswitch_(S_box_leader)). To infer the couplings with an RNA alphabet (.ACGU) type the following in the base directory:

bin/plmc -c example/RNA/RF00162.EC -o example/RNA/RF00162.params -a .ACGU -le 20.0 -lh 0.01 -m 50 example/RNA/RF00162.fasta

To plot the aggregated coupling scores type the following in MATLAB from the `scripts` directory:

params = read_params('../example/RNA/RF00162.params');
 plot_coupling_scores(params)
<img src="example/RNA/RF00162.png" width="500">

The default alphabet (-ACDEFGHIKLMNPQRSTVWY) can be overridden by the option `-a ALPHABET`. All uppercase letters and non-letter ASCII characters are acceptable. Lowercase letters in the alignment file will be mapped to the corresponding uppercase letter, except for in focus mode `-f`, in which columns that are lower case in the focus sequence will be discarded.

**Physical systems**. As an example, simulated draws from a 3-state, 1-dimensional Potts model are provided in the examples folder and encoded by the characters _, *, and ^. The following command would estimate the parameters by running to convergence with λe = 1.0, λh = 1.0 and sequence reweighting disabled:

bin/plmc -c example/potts/potts3.txt -a _*^ -t -1 -le 1.0 -lh 1.0 example/potts/potts3.a2m
A 1D Potts model will only have interactions between i -> i + 1, which should be evident in the coupling summary scores output to example/potts/potts3.txt

## References
The use of pseudolikelihood approximations for approximate inference of spin models for sequence families was established in the compsci/bioinformatics literature by

Balakrishnan, S., Kamisetty, H., Carbonell, J. G., Lee, S. I., & Langmead, C. J. (2011). [Learning generative models for protein fold families](http://onlinelibrary.wiley.com/doi/10.1002/prot.22934/abstract). Proteins: Structure, Function, and Bioinformatics, 79(4), 1061-1078.

and in the biophysics literature by

Ekeberg, M., Lövkvist, C., Lan, Y., Weigt, M., & Aurell, E. (2013). [Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models](http://journals.aps.org/pre/abstract/10.1103/PhysRevE.87.012707). Physical Review E, 87(1), 012707.

`plmc` implements a joint optimization version of inference described in these and subsequent works (i.e. the 'symmetric' pseudolikelihood). If you'd like to use `plmc` in your own work, please cite the following paper. Also, please let us know if you have any comments or questions!

Hopf, T. A., Ingraham, J. B., Poelwijk, F. J., Schärfe, C. P., Springer, M., Sander, C., & Marks, D. S. (2017). [Mutation effects predicted from sequence co-variation](https://www.nature.com/nbt/journal/v35/n2/abs/nbt.3769.html). Nature Biotechnology, 35(2), 128-135.

## Author
plmc was written by [John Ingraham](mailto:john.ingraham@gmail.com) in [Debora Marks' lab](https://marks.hms.harvard.edu/) at Harvard Medical School

## Credits
This code uses a [C implementation of L-BFGS by Naoaki Okazaki](https://github.com/chokkan/liblbfgs "libLBFGS") and [Nishimura and Matsumoto's Mersenne Twister in C](http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html), which are included in this repo.

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