LS-GKM: A new gkm-SVM software for large-scale datasets

gkm-SVM, a sequence-based method for predicting regulatory DNA elements, is a useful tool for studying gene regulatory mechanisms. In continuous efforts to improve the method, new software, LS-GKM, is introduced. It offers much better scalability and provides further advanced gapped k-mer based kernel functions. As a result, LS-GKM achieves considerably higher accuracy than the original gkm-SVM.

Citation

Please cite the following paper if you use LS-GKM in your research:

• Ghandi, M.†, Lee, D.†, Mohammad-Noori, M. & Beer, M. A. Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features. PLoS Comput Biol 10, e1003711 (2014). doi:10.1371/journal.pcbi.1003711 † Co-first authors

• Lee, D. LS-GKM: A new gkm-SVM for large-scale Datasets. Bioinformatics btw142 (2016). doi:10.1093/bioinformatics/btw142

Installation

After downloading and extracting the source codes, type:

$ cd src
$ make 

If successful, You should be able to find the following executables in the current (src) directory:

gkmtrain
gkmpredict

make install will simply copy these two executables to the ../bin direcory

Tutorial

We introduce the users to the basic workflow of LS-GKM. Please refer to help messages for more detailed information of each program. You can access to it by running the programs without any argument/parameter.

Training of LS-GKM

You train a SVM classifier using gkmtrain. It takes three arguments; positive sequence file, negative sequence file, and prefix of output.

Usage: gkmtrain [options] <posfile> <negfile> <outprefix>

 train gkm-SVM using libSVM

Arguments:
 posfile: positive sequence file (FASTA format)
 negfile: negative sequence file (FASTA format)
 outprefix: prefix of output file(s) <outprefix>.model.txt or
            <outprefix>.cvpred.txt

Options:
 -t <0 ~ 5>   set kernel function (default: 4 wgkm)
              NOTE: RBF kernels (3 and 5) work best with -c 10 -g 2
                0 -- gapped-kmer
                1 -- estimated l-mer with full filter
                2 -- estimated l-mer with truncated filter (gkm)
                3 -- gkm + RBF (gkmrbf)
                4 -- gkm + center weighted (wgkm)
                     [weight = max(M, floor(M*exp(-ln(2)*D/H)+1))]
                5 -- gkm + center weighted + RBF (wgkmrbf)
 -l <int>     set word length, 3<=l<=12 (default: 11)
 -k <int>     set number of informative column, k<=l (default: 7)
 -d <int>     set maximum number of mismatches to consider, d<=4 (default: 3)
 -g <float>   set gamma for RBF kernel. -t 3 or 5 only (default: 1.0)
 -M <int>     set the initial value (M) of the exponential decay function
              for wgkm-kernels. max=255, -t 4 or 5 only (default: 50)
 -H <float>   set the half-life parameter (H) that is the distance (D) required
              to fall to half of its initial value in the exponential decay
              function for wgkm-kernels. -t 4 or 5 only (default: 50)
 -R           if set, reverse-complement is not considered as the same feature
 -c <float>   set the regularization parameter SVM-C (default: 1.0)
 -e <float>   set the precision parameter epsilon (default: 0.001)
 -w <float>   set the parameter SVM-C to w*C for the positive set (default: 1.0)
 -m <float>   set cache memory size in MB (default: 100.0)
              NOTE: Large cache signifcantly reduces runtime. >4Gb is recommended
 -s           if set, use the shrinking heuristics
 -x <int>     set N-fold cross validation mode (default: no cross validation)
 -i <int>     run i-th cross validation only 1<=i<=ncv (default: all)
 -r <int>     set random seed for shuffling in cross validation mode (default: 1)
 -v <0 ~ 4>   set the level of verbosity (default: 2)
                0 -- error msgs only (ERROR)
                1 -- warning msgs (WARN)
                2 -- progress msgs at coarse-grained level (INFO)
                3 -- progress msgs at fine-grained level (DEBUG)
                4 -- progress msgs at finer-grained level (TRACE)
-T <1|4|16>   set the number of threads for parallel calculation, 1, 4, or 16
                 (default: 1)

First try to train a model using simple test files. Type the following command in tests/ directory:

$ ../bin/gkmtrain wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.tr.fa wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.neg.tr.fa test_gkmtrain

It will generate test_gkmtrain.model.txt, which will then be used for scoring of any DNA sequences as described below. This result should be the same as wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.model.txt

You can also perform cross-validation (CV) analysis with -x <N> option. For example, the following command will perform 5-fold CV.

$ ../bin/gkmtrain -x 5 wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.tr.fa wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.neg.tr.fa test_gkmtrain

The result will be stored in test_gkmtrain.cvpred.txt, and this should be the same as wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.cvpred.txt

Please note that it will run SVM training N times, which can take time if training sets are large. In this case, you can perform CV analysis on a specific set by using -i <I> option for parallel runnings. The output will be <outprefix>.cvpred.<I>.txt

The format of the cvpred file is as follows:

[sequenceid] [SVM score] [label] [CV-set]
...

Scoring DNA sequence using gkm-SVM

You use gkmpredict to score any set of sequences.

Usage: gkmpredict [options] <test_seqfile> <model_file> <output_file>

 score test sequences using trained gkm-SVM

Arguments:
 test_seqfile: sequence file for test (fasta format)
 model_file: output of gkmtrain
 output_file: name of output file

Options:
 -v <0|1|2|3|4>  set the level of verbosity (default: 2)
                   0 -- error msgs only (ERROR)
                   1 -- warning msgs (WARN)
                   2 -- progress msgs at coarse-grained level (INFO)
                   3 -- progress msgs at fine-grained level (DEBUG)
                   4 -- progress msgs at finer-grained level (TRACE)
-T <1|4|16>      set the number of threads for parallel calculation, 1, 4, or 16
                 (default: 1)

Here, you will try to score the positive and the negative test sequences. Type:

$ ../bin/gkmpredict wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.test.fa wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.model.txt test_gkmpredict.txt
$ ../bin/gkmpredict wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.neg.test.fa wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0.model.txt test_gkmpredict.neg.txt

Generating weight files for deltaSVM

You need to generate all possible non-redundant k-mers using the Python script scripts/nrkmers.py. Then, you score them using gkmpredict as described above. The output of lgkmpredict can be directly used by the deltaSVM script deltasvm.pl available from our deltasvm website.

** Please email Dongwon Lee (dongwon.lee AT childrens DOT harvard DOT edu) if you have any questions. **