Access the recommendation on F1000Prime

Please cite the PWMScan tool as follows:

  • Ambrosini G., Groux R., and Bucher P.,
    PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
    Bioinformatics 2018; 34(14): 2483-2484
To properly cite the PWMTools project, please use the Website citation as follows:
  • Ambrosini G., PWMTools,

In addition, users should cite the motif database used for the analysis, using the publication list here below.

Tools and Methods


Indexing Strategies for Rapid Searches of Short Words in Genome Sequences
Iseli C, Ambrosini G, Bucher P, and Jongeneel CV.
PLoS ONE. 2007; 2(6): e579.


Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Langmead et al.
Genome Biol 2009; 10: R25.


MAMOT: hidden Markov modeling tool
Schütz F, Delorenzi M.
Bioinformatics 2009; 24: 1399-1400.

PWM databases


JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
Kahn A et al.
Nucleic Acids Res. 2018; 46: D260-D266. DOI:10.1093/nar/gkx1126

HOCOMOCO V11 Human and Mouse

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
Kulakovskiy I et al.
Nucleic Acids Res. 2018; 44: D116-D125.

Isakova 2017 SMiLE-seq (Human, Mouse, and Fruit Fly)

SMiLE-seq identifies binding motifs of single and dimeric transcription factors
Isakova A et al.
Nat Methods 2017; 14(3): 316-322. DOI: 10.1038/nmeth.4143

Jolma2013 Human and Mouse HT-SELEX

DNA-binding specificities of human transcription factors
Jolma A et al.
Cell. 2015; 152(1-2): 327-39.

SwissRegulon (Human, Mouse, and Yeast)

SwissRegulon: a database of genome-wide annotations of regulatory sites
Pachkov M et al.
Nucleic Acids Res. 2007; 35(Database issue): D127-31. DOI: 10.1093/nar/gkl857

Mouse and Worm UniPROBE

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions
Hume MA et al.
Nucleic Acids Res. 2015; 43(Database issue): D117-22.

Drosophila OnTheFly 2014

OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites
Shazman S et al.
Nucleic Acids Res. 2014; 42(Database issue): D167-71.

Arabidopsis DAPv1

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
O'Malley RC et al.
Cell. 2016; 165(5): 1280-92.


Determination and inference of eukaryotic transcription factor sequence specificity
Weirauch MT et al.
Cell. 2014; 158(6): 1431-1443. DOI: 10.1016/j.cell.2014.08.009

The MEME Suite

The MEME Suite
Bailey TL, Johnson J, Grant CE, Noble WS.
Nucleic Acids Res. 2015; 43(W1): W39-49.
Original Paper PMID:19458158
MEME SUITE: tools for motif discovery and searching
Bailey TL et al.
Nucleic Acids Res. 2009; 37(Web Server issue): W202-8.

Last update April 2021