Two Sample Logo protocols

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Two Sample Logo specifications

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Unique identifier OMICS_05890
Name Two Sample Logo
Interface Web user interface
Restrictions to use None
License MIT License
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Two Sample Logo

Two Sample Logo in pipeline

2017
PMCID: 5702851
PMID: 29213239
DOI: 10.3389/fphar.2017.00854

[…] 3730 dna analyzer (applied biosystems, ma, usa). the primers used for sanger sequencing validation of called sites were listed in supplementary table . sequence logos were generated with the program two sample logo (vacic et al., )., tophat v2.1.0 was used with default parameters to generate acceptable alignments for cufflinks, in which the rna-seq paired-end reads were aligned […]


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Two Sample Logo in publications

 (15)
PMCID: 5702851
PMID: 29213239
DOI: 10.3389/fphar.2017.00854

[…] 3730 dna analyzer (applied biosystems, ma, usa). the primers used for sanger sequencing validation of called sites were listed in supplementary table . sequence logos were generated with the program two sample logo (vacic et al., )., tophat v2.1.0 was used with default parameters to generate acceptable alignments for cufflinks, in which the rna-seq paired-end reads were aligned […]

PMCID: 5724017
PMID: 28928222
DOI: 10.1074/jbc.M117.810945

[…] experiment described in , see under “experimental procedures.” a list of putative n-glycosylation sites and the voting classifier predictions are shown in supplemental table s3. we performed a two-sample logo visualization on the output (d). as expected, the trends in this plot are similar to those generated from the glycoproteomics data alone (c)., although tbstt3c (tb927.5.910) […]

PMCID: 5071865
PMID: 27762281
DOI: 10.1038/srep35432

[…] of amino acids near lysine residue was also analyzed using weblogo. to compare neighboring residues in the methylated and non methylated lysines in the proteomics identified proteins, we used two sample logo., go enrichment was performed for functional classification and cellular localization of the methylated proteins using plasmodb (version 13.0)., we downloaded the string […]

PMCID: 4917084
PMID: 27332813
DOI: 10.1371/journal.pone.0157896

[…] phosphorylation and reference sites are found in more than one tissue. the statistics of the resulting dataset, ps1d-70, can be found in (11097 phosphorylation sites in 5286 proteins)., we used the two sample logo method [] to find enriched and depleted residues in the 21-mer sequences occurring in different tissues, using the associated psss/ptss/pyss and non-pss/non-ptss/non-pyss as positive […]

PMCID: 4855882
PMID: 27143130
DOI: 10.1186/s12977-016-0266-9

[…] atf-creb (330–337), c/ebp-i (338–349), nf-κb-ii (350–359), nf-κb-i (363–373), sp-iii (377–386), sp-ii (388–398), and sp-i (399–408), as well as the rna stem loop (454–518), were evaluated using two sample logo []. two sample logo is a web-based application that calculates and visualizes the differences between two sets of aligned sequences. each nucleotide was represented with a different […]


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Two Sample Logo institution(s)
Computer Science and Engineering Department, University of California Riverside, CA, USA

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