Review of different sequence motif finding algorithms

FA Hashim, MS Mabrouk… - Avicenna journal of …, 2019 - pmc.ncbi.nlm.nih.gov
The DNA motif discovery is a primary step in many systems for studying gene function. Motif
discovery plays a vital role in identification of Transcription Factor Binding Sites (TFBSs) that …

How does DNA sequence motif discovery work?

P D'haeseleer - Nature biotechnology, 2006 - nature.com
How does DNA sequence motif discovery work? | Nature Biotechnology Skip to main content
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The MEME suite

TL Bailey, J Johnson, CE Grant… - Nucleic acids …, 2015 - academic.oup.com
The MEME Suite is a powerful, integrated set of web-based tools for studying sequence
motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their …

DREME: motif discovery in transcription factor ChIP-seq data

TL Bailey - Bioinformatics, 2011 - academic.oup.com
Abstract Motivation: Transcription factor (TF) ChIP-seq datasets have particular
characteristics that provide unique challenges and opportunities for motif discovery. Most …

JASPAR: an open‐access database for eukaryotic transcription factor binding profiles

A Sandelin, W Alkema, P Engström… - Nucleic acids …, 2004 - academic.oup.com
The analysis of regulatory regions in genome sequences is strongly based on the detection
of potential transcription factor binding sites. The preferred models for representation of …

Discovering motifs in ranked lists of DNA sequences

E Eden, D Lipson, S Yogev… - PLoS computational …, 2007 - journals.plos.org
Computational methods for discovery of sequence elements that are enriched in a target set
compared with a background set are fundamental in molecular biology research. One …

Assessing computational tools for the discovery of transcription factor binding sites

M Tompa, N Li, TL Bailey, GM Church, B De Moor… - Nature …, 2005 - nature.com
The prediction of regulatory elements is a problem where computational methods offer great
hope. Over the past few years, numerous tools have become available for this task. The …

STAMP: a web tool for exploring DNA-binding motif similarities

S Mahony, PV Benos - Nucleic acids research, 2007 - academic.oup.com
STAMP is a newly developed web server that is designed to support the study of DNA-
binding motifs. STAMP may be used to query motifs against databases of known motifs; the …

A survey on deep learning in DNA/RNA motif mining

Y He, Z Shen, Q Zhang, S Wang… - Briefings in …, 2021 - academic.oup.com
DNA/RNA motif mining is the foundation of gene function research. The DNA/RNA motif
mining plays an extremely important role in identifying the DNA-or RNA-protein binding site …

[HTML][HTML] PWM2Vec: An efficient embedding approach for viral host specification from coronavirus spike sequences

S Ali, B Bello, P Chourasia, RT Punathil, Y Zhou… - Biology, 2022 - mdpi.com
Simple Summary The family of coronaviruses comprises a diverse set of strains and variants
which cause diseases from the common cold to COVID-19. Moreover, they infect a wide …