PWMTools

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, bty127
To properly cite the PWMTools project, please use the Website citation as follows:
  • Ambrosini G., PWMTools, http://ccg.vital-it.ch/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

PMID:18440999
MAMOT: hidden Markov modeling tool
Schütz F, Delorenzi M.
Bioinformatics 200924: 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 Jul 1; 43(W1):W39-49.
Original Paper PMID:19458158
MEME SUITE: tools for motif discovery and searching
Bailey TL et al.
Nucleic Acids Res. 2009 Jul; 37(Web Server issue):W202-8.
Last update March 2018