PWMTools
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Due to maintenance activity, PWMTools might not be fully operational these days. Please contact us in case of problems.

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 2016

PMID:26531826
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
Mathelier A et al.
Nucleic Acids Res. 2016; 44(Database issue): D110-D115.

JASPAR CORE 2014

PMID:24194598
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
Mathelier A et al.
Nucleic Acids Res. 2014; 42(Database issue): D142-7.

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.

Jolma2013 Human and Mouse HT-SELEX

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

HOCOMOCO V9 Human

PMID:23175603
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
Kulakovskiy I et al.
Nucleic Acids Res. 2013; 41(Database issue): D195-202.

HOCOMOCO V10 Human and Mouse

PMID:26586801
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
Kulakovskiy I et al.
Nucleic Acids Res. 2016; 44(Database issue): D116-25.

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.

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 Papaer 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 October 2017