PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Author:

Ambrosini Giovanna12,Groux Romain12,Bucher Philipp12

Affiliation:

1. The Swiss Institute for Experimental Cancer Research (ISREC), Swiss Federal Institute of Technology Lausanne (EPFL)

2. Swiss Institute of Bioinformatics, Lausanne, Switzerland

Funder

Swiss Institute of Bioinformatics

Swiss Federal Institute of Technology Lausanne

EPFL

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Reference5 articles.

1. The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data;Ambrosini;BMC Genomics,2016

2. MEME Suite: tools for motif discovery and searching;Bailey;Nucleic Acids Res,2009

3. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework;Khan;Nucleic Acids Res,2017

4. HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis;Kulakovskiy;Nucleic Acids Res,2017

5. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome;Langmead;Genome Biol,2009

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