STAMP protocols

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STAMP specifications

Information


Unique identifier OMICS_08107
Name STAMP
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for STAMP

STAMP in pipelines

 (5)
2017
PMCID: 5606997
PMID: 28931820
DOI: 10.1038/s41467-017-00578-5

[…] levels observed in fam46cmut-gfp cells. functional clustering of go terms analysis was performed using david. the search for common sequence motif was performed using homer and further analyzed by stamp., multiple alignments analyses were performed using profile alignement (praline) (http://ibivu.cs.vu.nl/programs/pralinewww/), ., ms analysis were performed essentially as described. briefly, […]

2017
PMCID: 5733009
PMID: 29312363
DOI: 10.3389/fpls.2017.02049

[…] the statistically-significant motifs were screened for similarity with known transcription factor binding motifs using poxo (kankainen et al., ) (http://ekhidna.biocenter.helsinki.fi/poxo) and stamp (mahony and benos, )., promoters of nrrs genes identified along with the previously reported genes as positive control (tobrb7, atcel1, hahsp17, and lemmi9) were subjected to comparative […]

2014
PMCID: 4188601
PMID: 25289637
DOI: 10.1371/journal.pone.0109326

[…] and intronic hcnes, respectively., to investigate possible tfbss within hcnes, we identified overrepresented heptamers in hcnes sequences and queried the top 50 against flyreg motifs using stamp . to identify overrepresented heptamers, we computed the binomial probability of whether their observed frequency in hcnes is higher than expected by chance. we estimated the expected frequency […]

2014
PMCID: 5154493
PMID: 24965723
DOI: 10.1038/srep05454

[…] a method via comparison with the transfac database. first, our computationally determined tfbs motifs were mapped to all those 199 experimentally verified plant tfbs motifs in transfac using stamp (e-value cutoff 1e-5). for each of the tfbs motifs, the best-hit plant motif in transfac was defined as its “similar motif”. next, the tf proteins binding to this “similar motif” […]

2010
PMCID: 3091678
PMID: 20920248
DOI: 10.1186/1471-2164-11-527

[…] way as the 27 lexa protein tree., the phylogenetic tree (figure s1 in additional file ) of lexa-binding sites in cyanobacteria, b. subtilis, α-proteobacteria and e. coli k12 was generated by the stamp web tool [] with the default alignment parameters: pearson correlation coefficient for column comparison metric; ungapped smith-waterman for pair-wise alignment. the phylogenetic tree […]


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STAMP in publications

 (71)
PMCID: 5733009
PMID: 29312363
DOI: 10.3389/fpls.2017.02049

[…] genes to identify nrrs motif (supplementary figure presentation ; supplementary figure ). to identify the transcription factors that might bind to these sites, we used poxo (kankainen et al., ) and stamp (mahony and benos, ) but no statistically significant similarity to known motifs was found. therefore, further characterization of these novel motifs is required to establish their functional […]

PMCID: 5673197
PMID: 29107972
DOI: 10.1371/journal.pone.0187625

[…] with the density function from the r core package []. dreme [] was used for motif discovery with the 1000 bp sequences upstream of putative transcription start sites from the reference genome. stamp [] was used for dna motif matching., the authors would like to thank rene corral, emily delorean, jillian lang, paul langlois, bradley tonnessen, jesse ellgren, and troy aubol for technical […]

PMCID: 5640250
PMID: 29028826
DOI: 10.1371/journal.pone.0186435

[…] genes in a. gambiae, in vivo and in vitro. therefore, we investigated which other motifs co-occur with this type. focusing on siomics-detected crms containing a motif with the better matching stamp e value (9.2 x10-8) to the dorsal (dl)-type tfbs, the following rel potential partners were identified: rel, stat, lola and deaf1. these findings suggest that agdeaf1 and aglola are robust […]

PMCID: 5606997
PMID: 28931820
DOI: 10.1038/s41467-017-00578-5

[…] levels observed in fam46cmut-gfp cells. functional clustering of go terms analysis was performed using david. the search for common sequence motif was performed using homer and further analyzed by stamp., multiple alignments analyses were performed using profile alignement (praline) (http://ibivu.cs.vu.nl/programs/pralinewww/), ., ms analysis were performed essentially as described. briefly, […]

PMCID: 5569996
PMID: 28854641
DOI: 10.1093/gbe/evx127

[…] the mean auc. only motifs with a nes above a specified threshold (default 2.5) are considered enriched. to simplify the output, the enriched motifs are grouped into clusters of similar motifs using stamp (). motifs assigned to the same cluster are given the same color in the results table. to retrieve an optimal subset of the input gene set as putative target genes, a “leading edge” […]


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STAMP institution(s)
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA

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