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Seeder specifications

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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

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  • person_outline Marti V. Strömvik

Publication for Seeder

Seeder citations

 (7)
library_books

De novo computational identification of stress related sequence motifs and microRNA target sites in untranslated regions of a plant translatome

2017
Sci Rep
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 […]

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

[…] amino acid metabolism. the 1000 bp upstream flanking regions of the differentially expressed genes were analysed and nine overrepresented motifs were found using three motif discovery algorithms (seeder, weeder and meme). these results point to coordinated gene regulation at the transcriptional level controlling steady state potato responses to n sufficiency., potatoes (solanum tuberosum l.), […]

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

[…] was obtained for each species as the number of dehydrins used in this study. the sequences were downloaded using ncbi entrez direct e-utilities []., 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 […]

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

[…] 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 […]

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

[…] 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 […]

library_books

Identification of novel motif patterns to decipher the promoter architecture of co expressed genes in Arabidopsis thaliana

2013
BMC Syst Biol
PMCID: 3852273
PMID: 24555803
DOI: 10.1186/1752-0509-7-S3-S10

[…] specific) composed of background genomic promoters other than those of genes in the subsets: motif-prediction set and model-build set was formed., we used three different motif-discovery programs: seeder [], weeder [] and meme []. for seeder [], motifs 6bp, 8bp, 10bp and 12bp long with a seed length of 7 were predicted. several runs were done regarding both strands. weeder [] was also run […]


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

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