Weeder statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left De novo motif discovery chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

Weeder specifications

Information


Unique identifier OMICS_07763
Name Weeder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Giulio Pavesi <>

Information


Unique identifier OMICS_07763
Name Weeder
Interface Web user interface
Restrictions to use None
Input data Sequence
Input format FASTA
Programming languages C++
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Giulio Pavesi <>

Publications for Weeder

Weeder in pipelines

 (4)
2014
PMCID: 4352135
PMID: 25517099
DOI: 10.1038/nature14021

[…] redundant terms. co-occurrence between our datasets and previously published datasets was visualized with genevenn and bioinforx area-proportional venn diagram., we used two distinct algorithms, weeder and fire to perform an unbiased search for overrepresented sequences in the promoters of skn-1-regulated genes that were identified by sam. we submitted upstream sequences (1000 bp) to weeder […]

2011
PMCID: 3171486
PMID: 21931761
DOI: 10.1371/journal.pone.0024576

[…] which were 500 bp flanking the binding sites of these long motifs., to obtain the optimal results, the motif lengths were adjusted accordingly in several tools. the motif length for amadeus and weeder was set to 12 because this is the maximal motif length allowed. the motif length for mdscan was set to 12 and 20, respectively. to control the total running time with limited computational […]

2009
PMCID: 2714311
PMID: 19534778
DOI: 10.1186/1471-2202-10-60

[…] of the family as the queries. for phylogenic analysis, mrna sequences were translated into amino acid sequences. the analyses for conserved motifs were performed by the scan for matches [], weeder [] and jasper []. multiple alignment of pmp22 was performed by lagan [] and presented by vista []., pmp22: peripheral myelin protein 22; cmt1a: charcot-marie-tooth disease type1a; ncv: nerve […]

2008
PMCID: 2577007
PMID: 18997859
DOI: 10.1371/journal.pone.0003645

[…] could be considered high stringency (pwm log-odds>8.5), whereas 38 of 60 (63%) contained ares with low stringency (pwm log-odds>5.0). de novo approaches utilizing bioprospector , mdscan and weeder algorithms yielded a total of 525 recurring motifs within the 60 l1 arors. to collapse the many similar motifs into similarity groups, we employed linear hierarchical clustering based […]


To access a full list of citations, you will need to upgrade to our premium service.

Weeder in publications

 (63)
PMCID: 5695801
PMID: 29155860
DOI: 10.1371/journal.pone.0187891

[…] short sequence motifs in enriched peaks, we used total 100nt sequences (from peak summit, 50bp down and 50bp up). we used top 1000 peaks (based on fold change) for finding motifs using both weeder [] and meme [] programs., possible occurrence of tf motifs in peak regions (150bp around peak summit), or in target gene promoters were predicted with storm algorithm [] with a p-value cutoff […]

PMCID: 5578634
PMID: 28859164
DOI: 10.1371/journal.pone.0184185

[…] with fdr values < 0.05 from the edger analysis were used as the foreground sequences, while those with fdr values > 0.4 were used as the background sequences. amd [], glam2 [], dreme [], and weeder [] were used to find the de novo consensus motifs. the occurrences of motifs were examined by fimo []. the jaspar database, version 2014 (http://jaspar2014.genereg.net/) was used to search […]

PMCID: 5494305
PMID: 28658625
DOI: 10.1016/j.celrep.2017.06.011

[…] were associated with genes by annotating the nearest transcription start site ± 100 kb. functional annotation analysis was performed using david (, ). de novo motif discovery was performed using weeder () for ta and tbx16 peaks and dreme () for mixl1., data for morphant embryos were generated at shield (6 hpf) and 90% epiboly (9 hpf) using agilent zebrafish gene expression microarrays (v3) […]

PMCID: 5343461
PMID: 28276452
DOI: 10.1038/srep43861

[…] level in arabidopsis thaliana under normal and stressed conditions. the test group of sequences was divided into random subgroups and subjected to three de novo motif finding algorithms (seeder, weeder and meme). in addition to identifying sequence motifs, using an in silico tool we have predicted microrna target sites in the 3′ utrs of the translationally regulated genes, as well […]

PMCID: 5886188
PMID: 28335003
DOI: 10.1093/hmg/ddx092

[…] analysis steps are documented in the . briefly, we carried out de novo motif analysis using multiple parallel approaches: meme-chip () from the meme suite (), xxmotif () and pscanchip () from the weeder/modtools suite (). for the meme-chip and xxmotif analyses, we used the peak intervals in cpo10 and extracted the sequence underlying each interval ± 150bp from a repeat-masked version […]


To access a full list of publications, you will need to upgrade to our premium service.

Weeder institution(s)
University of Milan, Italy

Weeder review

star_border star_border star_border star_border star_border
star star star star star
Anonymous user #1600's avatar image No country

Anonymous user #1600

star_border star_border star_border star_border star_border
star star star star star
Desktop
I wrote a review on Biostars about Weeder2:
https://www.biostars.org/p/116633/