seqLogo protocols

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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 1.46.0
Stability Stable
Requirements
methods, grid, stats4
Maintained Yes

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Documentation


Maintainer


  • person_outline Oliver Bembom <>

seqLogo in pipelines

 (6)
2017
PMCID: 5363513
PMID: 28325297
DOI: 10.1016/j.omtn.2017.02.002

[…] single site. to improve data quality, we discarded all sites supported by less than ten reads. the sequence logos for the nucleotide composition around the integration sites were generated with the seqlogo package in r. to compute the representation of the insertion sites in various annotated segments of the human genome, databases for various genomic features were downloaded from the ucsc […]

2016
PMCID: 5388426
PMID: 28180286
DOI: 10.1093/nar/gkw969

[…] those at positions with identified mutations. misincorporation hotspots for the ecδgre and scδtfiis datasets were defined as having >50 misincorporations. sequence logos were created using the r seqlogo package ()., generic feature format version 3 files (gff3) were downloaded from the ncbi website in order to identify protein coding regions (cdss). aligned locations were identified […]

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. […]

2014
PMCID: 4217530
PMID: 25158628
DOI: 10.1038/ncomms5719

[…] tools implemented in meme-chip with default parameters. calculation of motif occurrences in test sequences and sequence logo generation were performed using the bioconductor packages biostrings and seqlogo, respectively (http://www.bioconductor.org)., j.a.w. performed mouse cell line experiments; a.c. performed human cell line experiments and participated in data analysis; b.h.a. helped develop […]

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 () and a modification of seqlogo (). 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 […]


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seqLogo in publications

 (63)
PMCID: 5868767
PMID: 29579047
DOI: 10.1371/journal.pone.0192851

[…] shows three examples of sequences that were disregarded because they did not behave as the rest of the members in the superfamily (see ). sequence logo plots were generated with the program seqlogo [] for all filtered alignments focusing on the positions of the functional residues ()., the full sequences of all proteins in the superfamily that passed our filtering criteria were used […]

PMCID: 5862974
PMID: 29563587
DOI: 10.1038/s41598-018-23342-1

[…] from a variant sequence were compared with those from a reference sequence. sequence logos for the position weight matrix of the binding consensus were created from transfac matrices using r library seqlogo., the rna-seq v2 data and clinical information of tcga lung adenocarcinoma (tcga-luad) was downloaded from the nci genomic data commons using tcga-assembler v2.0.1 (the data were downloaded […]

PMCID: 5836368
PMID: 29222161
DOI: 10.1074/mcp.RA117.000155

[…] each splice junctions in coding region (5′ or 3′ utrs were excluded) of protein coding transcripts from genome sequence. after calculating the nucleotide composition at each position, the r package seqlogo was used to plot the corresponding sequence logo for sequences 4 base pairs up- and downstream from the splicing site., mature human protein sequences from the abovementioned refseq […]

PMCID: 5719641
PMID: 29212449
DOI: 10.1186/s12863-017-0573-8

[…] and relative scores, for the neighboring g.92,377,635a > g sequence (± 20 bp) were analyzed with the jaspar database []. graphical representation of the frequency matrix was represented by seqlogo []., a luciferase reporter assay was conducted to determine if snps identified in the 5′-upstream region of the foxp3 gene might affect foxp3 expression. the 2364-bp fragment upstream […]

PMCID: 5814809
PMID: 29186616
DOI: 10.1093/nar/gkx1190

[…] with a slight modification of the default settings (maximum width: 10) (meme-chip version 4.10; http://meme.nbcr.net/meme/cgi-bin/meme-chip.cgi) (). the logo plots were generated using the r package seqlogo. mapping of tfbss to the specific genomic regions were calculated by the cisgenome. gene ontology (go) enrichment analysis was performed using the database for annotation, visualization, […]


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