Table 2 Brief description of 16 analyzed tools

TFBS prediction tools

Ciiider

A software which uses a combination of PWMs and MATCH algorithm to predict TFBSs

[89]

[33]

DWT-toolbox

A regulatory motif model that incorporates arbitrary pairwise dependencies between positions in binding sites using a Bayesian framework along with PSWMs

[90]

[106]

FIMO

Part of MEME-Suite package which search for individual occurrences of a motif in a DNA or protein sequence

[91]

[30]

HOMER

A software that can be implemented in UNIX operating systems, which offers a set of tools for motif discovery and analysis

[92]

[34]

INSECT 2.0

An online tool which allows the prediction of cis-regulatory modules (CRMs) at the genome level and long lists of genes. CRM search is done using PWMs available in databases

[93]

[35]

Matrix-scan

A part of regulatory sequence analysis tools (RSAT) which predicts TFBS using PWMs

[94]

[36]

MCAST

A part of the MEME-suite program which uses HMM with a p-value based scoring scheme to identify candidate CRMs which contain TFBSs

[95]

[65]

MOODS

A software implemented in C++ which uses advanced matrix matching algorithms to scan matrices against sequences

[96]

[32]

Morpheus

A web-based tool which allows using PWM models considering the dependencies between di or tri nucleotide positions

[97]

[37]

MotEvo

A software tool which uses a Bayesian probabilistic approach to predict TFBSs in multiple alignments of phylogenetically related DNA sequences

[98]

[68]

PWMScan

A web server which allows rapid scanning of genomes to match user-supplied or server-resident PWMs

[99]

[38]

TFBStools

A package based on R for the analysis and manipulation of TFBSs

[100]

[39]

De novo motif discovery tools

MEME

A part of MEME-suite which discovers novel-ungapped, recurring motifs of fixed length

[101]

[54]

MotifSampler

A tool based on the Gibbs sampling algorithm, which allows the identification of novel motifs

[102]

[51]

rGADEM

An R package based on GADEM software, which identifies novel motifs in large-scale genomic sequence data

[103]

[52]

STREME

A part of MEME-suite which identifies novel-ungapped, recurring motifs of fixed lengths that are relatively enriched

[104]

[53]