PWMTools

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 September 2017