From: A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data
Tool | Algorithm | Approach | Published year | Language | Operating system | Software features | Latest release version | Latest release year | Website | Maintenance | Ref. # |
---|---|---|---|---|---|---|---|---|---|---|---|
BayesPeak | BayesPeak algorithm | Used Hidden Markov model (HMM) for finding peaks | 2011 | R and C | Linux, Windows, and Mac OS X | Support multicore | 1.12.0 | N/A | http://compbio.sysbiol.cam.ac.uk/Resources/BayesPeak/csbayespeak.html | Yes | [54] |
BroadPeak | Maximal-segment algorithm, Gibbs sampling algorithm, Ruzzo–Tompa algorithm | Probabilistic model | 2013 | R | N/A | N/A | One version | 2013 | Yes | [55] | |
CisGenome | Two-pass algorithm | Implemented a modular design, use sliding window for peak detection | 2008 | C, C++ | Windows, Mac, and Linux | Stand-alone system, command mode and GUI | v2.0 | 2011 | Yes | [56] | |
DROMPA (DRaw and observe Multiple enrichment profiles and annotation) | Sliding window | Two-step procedure, DROMPA peak-calling program | 2013 | ANSI-C | Linux | N/A | 1.4.0 | 2013 | http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/drompa/ | Yes | [57] |
F-Seq | F-Seq density estimation algorithm | Kernel density estimation | 2008 | Java | Unix, Linux | N/A | 1.84 | 2011 | Yes | [58] | |
FindPeaks | Used directional reads module for identifying peaks | Implemented a modular architecture | 2008 | Java | Linux, Windows, and Mac OS X | Command line | 4.0 | N/A | Yes | [59] | |
GEM (Genome wide Event finding and Motif discovery) | Genome wide event finding and motif discovery (GEM) | Probabilistic model | 2012 | Java | N/A | Stand-alone software | 2.3 | 2013 | Yes | [60] | |
GLITR (GLobal Identifier of Target Regions) | GLITR algorithm | Used ChIP-Seq Peak Finder framework | 2009 | Perl and Python | N/A | N/A | N/A | N/A | N/A | N/A | [61] |
GLMNB (Negative binomial generalized linear model) | Sliding window | Generalized Linear Model with Negative binomial distribution | 2012 | N/A | N/A | N/A | 1.0 | 2012 | N/A | [62] | |
Hpeak (Hidden Markov model (HMM)-based Peak-finding algorithm) | HMM-based algorithm | Hidden Markov Model (HMM) | 2010 | Perl and C++ | Linux, Windows, and Mac OS | N/A | V2.1 | 2009 | N/A | [63] | |
MACS (Model-based analysis of ChIP-Seq) | MACS algorithm (use shift and sliding window algorithm) | Model-based Analysis of ChIP-Seq | 2008 | Python | Linux | stand-alone, no GUI, open source | 1.4.2 | 2012 | Yes | [64] | |
NEXT-peak (the normal-exponential two-peak) | NEXT-peak algorithm | Normal-exponential two-peak (NEXT-peak) model | 2013 | C++ | Linux | N/A | 1.1 | 2013 | Yes | [65] | |
PeakRanger | Same algorithm as PeakSeq for identifying broad regions. Summit-valley-alternator algorithm | Build the read coverage profile | 2011 | C++ | Linux, Mac OS, and Windows | Support parallel cloud computing | 1.16 | 2012 | Yes | [66] | |
PeakSeq | PeakSeq - two-pass strategy | Two-pass strategy | 2009 | C and Perl | N/A | N/A | 1.1 | 2011 | N/A | [67] | |
QuEST (Quantitative Enrichment of Sequence Tags) | Construct profiles and use shifting method | Statistical framework-Kernel Density Estimation approach | 2008 | C++ | Linux, Mac OS | Open source, non-profit use | 2.4 | 2009 | No | [68] | |
SeqSite | Two-step strategy: detect tag-enriched regions and then pinpoint binding sites in the detected regions | Poisson model | 2011 | C/C++ | Windows, Mac OS X, and Linux | Academic use only | 1.1.2 | 2010 | http://0-bioinfo-au-tsinghua-edu-cn.brum.beds.ac.uk/software/seqsite/ | Yes | [69] |
SICER | Scoring scheme | Spatial clustering approach | 2009 | Python | Linux, Unix | N/A | v1.1 | 2011 | Yes | [70] | |
SIPeS (Site Identification from Paired-end Sequencing) | SIPeS algorithm | Used dynamic fragment pileup value for peak calling | 2010 | C | Linux | Non-profit use | 2.0 | 2010 | http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS | N/A | [71] |
SISSRs (Site Identification from Short Sequence Reads) | Site Identification from Short Sequence Reads (SISSRs) algorithm | Sliding window | 2008 | Perl | Linux, UNIX | N/A | v1.4 | 2008 | N/A | [72] | |
Sole-Search | Sole-Search program | Implemented several different analysis steps for peak calling | 2010 | Java | N/A | Web-based software | N/A | N/A | N/A | No | [73] |
T-PIC (Tree shape Peak Identification for ChIP-Seq) | Tree shape Peak Identification for ChIP-Seq (T-PIC) algorithm | Tree-based statistics | 2011 | R and Perl | N/A | N/A | One version | 2011 | N/A | [74] | |
USeq | Collection of algorithms and software for peak calling | Implemented several different methods for peak calling | 2008 | Java | Linux, Mac OS X, and Windows | GUI | 8.6.6 | 2013 | Yes | [75] | |
W-ChIPeaks | PELT algorithm and BELT algorithm | Statistical methods control false discovery rate | 2011 | PHP, Perl, Java and C++ | N/A | Web tool | 1.0.1 | 2012 | Yes for BELT only | [76] | |
ZINBA (Zero-Inflated Negative Binomial Algorithm) | Zero-Inflated Negative Binomial Algorithm (ZINBA) | Statistical framework | 2011 | C and R | Mac OS X and Linux/Unix | Support multi-core clusters | 2.02.03 | 2012 | Yes | [77] |