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, https://epd.expasy.org/pwmtools

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

Tools and Methods

FetchGWI

PMID:17593978 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.

Bowtie

PMID:19261174 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Langmead et al. Genome Biol 2009; 10: R25.

MAMOT

DOI:18440999 MAMOT: hidden Markov modeling tool Schütz F, Delorenzi M. Bioinformatics 2009; 24: 1399-1400.

PWM databases

JASPAR CORE 2018

PMCID:PMC5753243 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

PMCID:PMC5753240 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)

PMID:28092692 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

PMID:23332764 DNA-binding specificities of human transcription factors Jolma A et al. Cell. 2015; 152(1-2): 327-39.

SwissRegulon (Human, Mouse, and Yeast)

PMCID:PMC1716717 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

PMID:25378322 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

PMID:24271386 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

PMID:27203113 Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape O'Malley RC et al. Cell. 2016; 165(5): 1280-92.

CIS-BP

PMID:25215497 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

PMID:25953851 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.