The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
STAMP: a web tool for exploring DNA-binding motif similarities
Open accessAbstract
STAMP is a newly developed web server that is designed to support the study of DNA-binding motifs. STAMP may be used to query motifs against databases of known motifs; the software aligns input motifs against the chosen database (or alternatively against a user-provided dataset), and lists of the highest-scoring matches are returned. Such similarity-search functionality is expected to facilitate the identification of transcription factors that potentially interact with newly discovered motifs. STAMP also automatically builds multiple alignments, familial binding profiles and similarity trees when more than one motif is inputted. These functions are expected to enable evolutionary studies on sets of related motifs and fixed-order regulatory modules, as well as illustrating similarities and redundancies within the input motif collection. STAMP is a highly flexible alignment platform, allowing users to 'mix-and-match' between various implemented comparison metrics, alignment methods (local or global, gapped or ungapped), multiple alignment strategies and tree-building methods. Motifs may be inputted as frequency matrices (in many of the commonly used formats), consensus sequences, or alignments of known binding sites. STAMP also directly accepts the output files from 12 supported motif-finders, enabling quick interpretation of motif-discovery analyses. STAMP is available at http://www.benoslab.pitt.edu/stamp.
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PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
WebLogo: A Sequence Logo Generator: Figure 1
Crooks, G. E., Hon, G., Chandonia, J.-M., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,386
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,982
Multiple sequence alignment with the Clustal series of programs
Chenna, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg500 · Cited by 4,875
A Statistical Method for Evaluating Systematic Relationships
Sokal, R. R., & Michener, C. D. (1958) · Biodiversity Heritage Library (Smithsonian Institution) · doi:10.5281/zenodo.16435756 · Cited by 4,416
Transcriptional regulatory code of a eukaryotic genome
Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., Hannett, N. M., Tagne, J.-B., Reynolds, D. B., Yoo, J., et al. (2004) · Nature · doi:10.1038/nature02800 · Cited by 2,143
TRANSFAC(R): transcriptional regulation, from patterns to profiles
Matys, V. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg108 · Cited by 1,985
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
Sandelin, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh012 · Cited by 1,790
Hertz, G. Z., & Stormo, G. D. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.7.563 · Cited by 1,243
Hughes, J. D., Estep, P. W., Tavazoie, S., & Church, G. M. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3519 · Cited by 1,010
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SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
Bravo González-Blas, C., De Winter, S., Hulselmans, G., Hecker, N., Matetovici, I., Christiaens, V., Poovathingal, S., Wouters, J., Aibar, S., & Aerts, S. (2023) · Nature Methods · doi:10.1038/s41592-023-01938-4 · Cited by 778
Harb, A., Krishnan, A., Ambavaram, M. M. R., & Pereira, A. (2010) · Plant Physiology · doi:10.1104/pp.110.161752 · Cited by 747
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
Wei, G., Badis, G., Berger, M. F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A. R., et al. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.106 · Cited by 568
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data
Bravo González-Blas, C., Minnoye, L., Papasokrati, D., Aibar, S., Hulselmans, G., Christiaens, V., Davie, K., Wouters, J., & Aerts, S. (2019) · Nature Methods · doi:10.1038/s41592-019-0367-1 · Cited by 456
Metadata
- Authors
- Mahony, S., & Benos, P. V.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-05-08
- Volume
- 35
- Issue
- Web Server
- Pages
- W253-W258
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2119804413
- Cited by
- 465
- References
- 32
- FWCI
- 9.70
- Type
- journal article
- Language
- en
- Open access
- gold
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