The DOI matches its Crossref record.
Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments
Abstract
Sumary: Two Sample Logo is a web-based tool that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments. In a typical scenario, two groups of aligned sequences will share a common motif but will differ in their functional annotation. The inclusion of the background alignment provides an appropriate underlying amino acid or nucleotide distribution and addresses intersite symbol correlations. In addition, the difference detection process is sensitive to the sizes of the aligned groups. Two Sample Logo extends WebLogo, a widely-used sequence logo generator. The source code is distributed under the MIT Open Source license agreement and is available for download free of charge. Availability: Contact: predrag@indiana.edu
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
Hornbeck, P. V., Zhang, B., Murray, B., Kornhauser, J. M., Latham, V., & Skrzypek, E. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1267 · Cited by 3,411
Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B., Skrzypek, E., Murray, B., Latham, V., & Sullivan, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1122 · Cited by 1,646
Designing of interferon-gamma inducing MHC class-II binders
Dhanda, S. K., Vir, P., & Raghava, G. P. (2013) · Biology Direct · doi:10.1186/1745-6150-8-30 · Cited by 837
Rolfe, M. D., Rice, C. J., Lucchini, S., Pin, C., Thompson, A., Cameron, A. D. S., Alston, M., Stringer, M. F., Betts, R. P., Baranyi, J., et al. (2012) · Journal of Bacteriology · doi:10.1128/jb.06112-11 · Cited by 711
Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence
Singh, H., Ansari, H. R., & Raghava, G. P. S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062216 · Cited by 384
Metadata
- Authors
- Vacic, V., Iakoucheva, L. M., & Radivojac, P.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-04-21
- Volume
- 22
- Issue
- 12
- Pages
- 1536-1537
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2141818629
- Cited by
- 535
- References
- 0
- FWCI
- 1.60
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. https://app.cochat.ai/papers/10.1093/bioinformatics/btl151
- The paper
- Vacic, V., Iakoucheva, L. M., & Radivojac, P. (2006). Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics. https://doi.org/10.1093/bioinformatics/btl151
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
