seqLogo statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool seqLogo
info

Tool usage distribution map

This map represents all the scientific publications referring to seqLogo per scientific context
info info

Associated diseases

info

Popular tool citations

chevron_left Sequence logo generation chevron_right
Want to access the full stats & trends on this tool?

Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Oliver Bembom

seqLogo citations

 (75)
call_split

Bioinformatic characterization of the Anoctamin Superfamily of Ca2+ activated ion channels and lipid scramblases

2018
PLoS One
PMCID: 5868767
PMID: 29579047
DOI: 10.1371/journal.pone.0192851
call_split See protocol

[…] members. 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 to run […]

library_books

Identification of potential regulatory mutations using multi omics analysis and haplotyping of lung adenocarcinoma cell lines

2018
Sci Rep
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. […]

library_books

Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity*

2017
PMCID: 5836368
PMID: 29222161
DOI: 10.1074/mcp.RA117.000155

[…] f 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. […]

call_split

Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle

2017
BMC Genet
PMCID: 5719641
PMID: 29212449
DOI: 10.1186/s12863-017-0573-8
call_split See protocol

[…] s, scores, 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 []. […]

library_books

JUNB governs a feed forward network of TGFβ signaling that aggravates breast cancer invasion

2017
Nucleic Acids Res
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, and I […]

library_books

Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence

2017
BMC Genomics
PMCID: 5698953
PMID: 29162050
DOI: 10.1186/s12864-017-4304-3

[…] motif assigned based on random probabilities between 0 and 0.145 (the maximum number of genes in the background gene set matching to any specific motif was 14.5%). Sequence motifs were plotted using seqLogo (v1.42.0). Network analysis for co-occurring motifs was performed using igraph (v1.0.1), and for age-regulated genes using GeneMania []. To identify candidate transcription factors that bind e […]


Want to access the full list of citations?

seqLogo reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review seqLogo