seqLogo pipeline

seqLogo specifications

Information


Unique identifier OMICS_10709
Name seqLogo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA matrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.36.0
Stability Stable
Requirements methods, grid
Maintained Yes

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Documentation


Maintainer


  • person_outline Oliver Bembom <>

seqLogo IN pipelines

 (3)
2014
PMCID: 4110516
PMID: 25001002
DOI: 10.1038/ncomms5370

[…] a nucleotide position weight matrix (pwm), and pwms from adjacent subarrays were merged assuming equal weight at overlapping positions. sequence logo plots were then generated using ggplot and seqlogo., to make a comprehensive dataset of known primate prdm9 zinc finger sequences, we combined the zfs sequenced in our study with those from berg et. al., auton et. al., and groeneveld et. al. […]

2012
PMCID: 3458573
PMID: 22753031
DOI: 10.1093/nar/gks640

[…] base counts and mismatch counts were performed using standard unix utilities, especially awk. subsequent analyses used r, including the add-on packages rcolorbrewer (40) and a modification of seqlogo (41). the sequence reads are available as unmapped bam files from the ncbi short-read archive under project accession srp012938., position-specific scoring matrices normally assume […]

2010
PMCID: 3046479
PMID: 21143862
DOI: 10.1186/gb-2010-11-12-r119

[…] locations followed by calculating nucleotide frequencies at each position relative to the fragmentation site, thus generating a positional weight matrix (pwm). the pwms then were imported into the seqlogo (oliver bembom, dept. of biostatistics, university of california, berkeley, 2008) package for bioconductor in r and used to generate positional information content (ic) and sequence logos […]

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