Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

By Giulio Pavesi, P. Mereghetti, Giancarlo Mauri, Graziano Pesole. Nucleic Acids Res., 2004

547 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fcfd0544a35714eb863b45d3230e87c75f441e2e

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Citations in the corpus

Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development (2008, methodology): “Analysis of circadian clock regulatory elements We employed four different strategies to identify potential motifs of interest: a trio of established motif discovery tools (stand-alone versions of AlignACE v2004 [88,89], Weeder v1.2 [90, 91 ], and MotifSampler v3.2 [92,93]) and an exhaustive in sili”
STAMP: a web tool for exploring DNA-binding motif similarities (2007, methodology): “Currently supported STAMP input formats include the output ﬁles from motif-ﬁnder programs like SOMBRERO (19), BioProspector (18), MDScan (20), AlignACE (21), MEME (22), Weeder (23), MotifSampler (24), YMF (25), ANN-Spec (26), Consensus (27), Improbizer and Co-Bind (28).”
STREME: Accurate and versatile sequence motif discovery (2020, methodology): “As do several existing motif discovery algorithms (e.g., Weeder [10], HOMER [5], STEME [12]), STREME makes use of a data structure called a generalized suﬃx tree [18].”
Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. (2011, methodology): “Sequence analysis of ChIP peaks was performed with the Weeder webtool (20,21) and the logo of the resulting CLEAR motif was elaborated by using WebLogo (85).”
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition (2011, background): “2) [16], an exhaustive enumeration algorithm that tests the enrichment of each motif among the input sequences.”
Sequence and chromatin determinants of cell-type–specific transcription factor binding (2012, methodology): “We also used Weeder to find the 50 most enriched 6-, 8-, and 10-bp motifs (allowing one mismatch) using human genome-wide k-mer frequencies as the background.”
The C. elegans TGF-β Dauer Pathway Regulates Longevity via Insulin Signaling (2007, unknown): “1.5 kb of promoter sequences from genes in each cluster were submitted to BioProspector [12] and Weeder [12] to identify overrepresented motifs; high-scoring motifs are depicted by WebLogo [31].”
GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis[W][OA] (2009, methodology): “GLK cis-Element To examine whether the promoters of GLK-regulated genes share a common cis-element, we analyzed the 23 ChIP-positive genes using Weeder, a program that uses a consensus-based method to search for conserved motifs in submitted sequences (Pavesi et al., 2004; Tompa et al., 2005).”
Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development[W] (2007, methodology): “MDscan (Liu et al., 2002) and Weeder (Pavesi et al., 2004) was also used to discover the novel consensus motif of HY5 binding target genes.”
Discovering Sequence Motifs with Arbitrary Insertions and Deletions (2008, methodology): “These include A-GLAM [1], AlignACE [2], BioProspector [3], MDscan [4], RSA Tools [5,6], Weeder [7] and YMF [8].”
Inferring direct DNA binding from ChIP-seq (2012, background): “We find that several ab initio motif discovery algorithms [Amadeus (6), DREME (3), MEME (22), Trawler (7) and WEEDER (23), see the Supplementary Data for details) applied to the NFIC (100 bp) ChIP-seq regions fail to discover a motif that matches the known in vitro motif, which has consensus TTGGCAN”