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motifStack specifications


Unique identifier OMICS_19821
Name motifStack
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.24.1
Stability Stable
methods, stats, RColorBrewer, grid, graphics, BiocGenerics, utils, Biostrings, BiocStyle, stats4, grDevices, RUnit, scales, knitr, ade4, R(>=2.15.1), htmlwidgets, XML, MotifDb, grImport, MotIV
Maintained Yes




No version available



  • person_outline Jianhong Ou

motifStack citations


Detection of hyper conserved regions in hepatitis B virus X gene potentially useful for gene therapy

PMCID: 5960815
DOI: 10.3748/wjg.v24.i19.2095

[…] 1 (nt or aa). for each window, the analysis computes the mean ic of each position within the window. in addition, the results are represented as sequence logos created using the r language package motifstack[]., the bioinformatics methods used in this study were reviewed by dr. josep gregori from the liver disease-viral hepatitis laboratory of vall d’hebron hospital (barcelona, spain), […]


Analysis of hepatitis B virus preS1 variability and prevalence of the rs2296651 polymorphism in a Spanish population

PMCID: 5807671
PMID: 29456407
DOI: 10.3748/wjg.v24.i6.680

[…] = log2 (20)- 4.322 = 0. these calculations in the regions of ntcp interaction (47 aa) and virion morphogenesis (22 aa) were also represented as sequence logos created using the r language package, motifstack[]., the statistical and bioinformatics methods used in this study were reviewed by dr. josep gregori from the liver disease-viral hepatitis laboratory (vall d’hebron institut […]


Abundant expression of somatic transposon derived piRNAs throughout Tribolium castaneum embryogenesis

Genome Biol
PMCID: 5613491
PMID: 28950880
DOI: 10.1186/s13059-017-1304-1

[…] reads were split equally between the possible targets., nucleotide frequencies of pirna reads at each position were calculated using a custom script, and sequence logos were plotted using the “motifstack” r package., ping-pong signatures were calculated following the procedure described in []. in brief, we extracted 25–35-nt sense–antisense read pairs and calculated the number […]


Transcription factor Hlx controls a systematic switch from white to brown fat through Prdm16 mediated co activation

Nat Commun
PMCID: 5507986
PMID: 28701693
DOI: 10.1038/s41467-017-00098-2

[…] algorithm) was downloaded from uniprobe database (, . the motif was trimmed by information content no less than 0.4 in both ends by r/bioconductor package motifstack (version 1.14.0). published prdm16 peaks of brown adipocytes were downloaded and annotated by r/bioconductor package chippeakanno (version 3.5.1). the sequences of the prdm16 peaks […]


Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants

BMC Genomics
PMCID: 5093975
PMID: 27806710
DOI: 10.1186/s12864-016-3202-4

[…] jordan being amongst the most highly expressed repeat elements in the sample., all sequence logos were based on the adapter- and quality score-trimmed reads, and were generated using the r package motifstack (ou and zhu, r package version 1.12.0)., all sequences of mirnas of v. carteri and c. reinhardtii (mirbase) were subjected to a multiple sequence alignment using clustalw []. the resulting […]


TSS EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens

BMC Genomics
PMCID: 5094136
PMID: 27806702
DOI: 10.1186/s12864-016-3211-3

[…] transtermhp v2.09 []. the program is run with standard parameter values, and an annotation file containing coordinates of all annotated genes., all sequence logos were generated with the r package motifstack from bioconductor, and using the background correction to adjust the signal according to gc content of the organism []., additional file 1: table s1. additional file 2: figure s1. […]

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