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Seeder specifications

Information


Unique identifier OMICS_06268
Name Seeder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Marti V. Strömvik

Publication for Seeder

Seeder citations

 (4)
library_books

The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs

2016
Sci Rep
PMCID: 4872257
PMID: 27193058
DOI: 10.1038/srep26090

[…] under-expressed in response to supplemented N. Motif discovery was performed separately for each set of differentially expressed genes.Three different programs were used for de novo motif discovery: Seeder v. 0.01, MEME v. 4.10.0 and Weeder v. 2.0. All three motif discovery programs were run simultaneously on Guillimin, Mcgill University’s high-performance computing server (http://www.hpc.mcgill. […]

library_books

De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes

2015
PLoS One
PMCID: 4482647
PMID: 26114291
DOI: 10.1371/journal.pone.0129016

[…] Motifs were discovered using MEME v4.9.1 [], Seeder v0.01 [] and Weeder v1.4.2 [], and using the five sets of sequences as separate input. Significant motifs were selected based on following parameters: E-value ≤ 0.05 for MEME, Q-value ≤ 0.01 fo […]

library_books

De novo prediction of cis regulatory elements and modules through integrative analysis of a large number of ChIP datasets

2014
BMC Genomics
PMCID: 4265420
PMID: 25442502
DOI: 10.1186/1471-2164-15-1047

[…] the actual locations of CREs need to be identified by a motif-finding tool [, ]. Although a few new motif-finders have been developed to analyze large sequence sets from ChIP-seq experiments, such as seeder [], Trawler [, ], ChIPMunk [], HMS [], CMF [], STEME [], DREME [], DECOD [], RSAT [], and POSMO [], they are typically used to find the CREs of a ChIP-ed TF in a short region of sequences (~200 […]

library_books

Discriminative Motif Discovery via Simulated Evolution and Random Under Sampling

2014
PLoS One
PMCID: 3923751
PMID: 24551063
DOI: 10.1371/journal.pone.0087670

[…] es the objective function to discriminate positive and negative sets of sequences based on this score and uses heuristic hill climbing to search the sequences for motifs that maximizes this function. Seeder is an integrated algorithm that combines the advantages of a pattern-driven method (used in seed PWM searching) and sequence-based method (used in PWM building) and identifies discriminative m […]

Citations

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Seeder institution(s)
Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, QC, Canada

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