Details

Title

Position weight matrix model as a tool for the study of regulatory elements distribution across the DNA sequence

Journal title

Archives of Control Sciences

Yearbook

2010

Issue

No 4

Authors

Divisions of PAS

Nauki Techniczne

Publisher

Committee of Automatic Control and Robotics PAS

Date

2010

Identifier

DOI: 10.2478/v10170-010-0028-1 ; ISSN 1230-2384

Source

Archives of Control Sciences; 2010; No 4

References

Gregory T. (2007), Eukaryotic genome size databases, Nucleic Acids Res, 35. ; Latchman D. (1997), Transcription factors: an overview, Int. J. Biochem. Cell Biol, 29, 1305. ; Karin M. (1990), Too many transcription factors: positive and negative interactions, New Biol, 2, 126. ; Roeder R. (1996), The role of general initiation factors in transcription by RNA polymerase II, Trends Biochem. Sci, 21, 327. ; Nikolov D. (1997), RNA polymerase II transcription initiation: a structural view, Proc. Natl. Acad. Sci. USA, 94, 15. ; Lee T. (2000), Transcription of eukaryotic protein-coding genes, Annu. Rev. Genet, 34, 77. ; Babu M. (2004), Structure and evolution of transcriptional regulatory networks, Curr. Opin. Struct. Biol, 14, 283. ; Brivanlou A. (2002), Signal transduction and the control of gene expression, Science, 295, 813. ; Levine M. (2003), Transcription regulation and animal diversity, Nature, 424, 147. ; Barthel K. (2008), A transcriptional enhancer from the coding region of ADAMTS5, PLoS One, 3. ; Gill G. (2001), Regulation of the initiation of eukaryotic transcription, Essays Biochem, 37, 33. ; Narlikar G. (2002), Cooperation between complexes that regulate chromatin structure and transcription, Cell, 108, 475. ; Xu L. (1999), Coactivator and corepressor complexes in nuclear receptor function, Curr. Opin. Genet. Dev, 9, 140. ; Wong J. (1994), TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs, Nucleic Acids Res, 22, 1890. ; Mukumoto F. (1993), DNA sequence requirement of a TATA element-binding protein from Arabidopsis for transcription in vitro, Plant Mol. Biol, 23, 995. ; Day W. (1992), Critical comparison of consensus methods for molecular sequences, Nucleic Acids Res, 20, 5, 1093. ; Claverie J. (1996), The statistical significance of nucleotide positionweight matrix matches, Comput. Appl. Biosci, 12, 431. ; Stormo G. (1982), Characterization of translational initiation sites in E. coli, Nucleic Acids Res, 10, 2971. ; Sandelin A. (2004), ConSite: web-based prediction of regulatory elements using cross-species comparison, Nucleic Acids Res, 32. ; Bucher P. (1990), Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences, J. Mol. Biol, 212, 563. ; Masuda K. (2005), Androgen receptor binding sites identified by a GREF_GATA model, J. Mol. Biol, 353, 763. ; Bernardi G. (2000), Isochores and the evolutionary genomics of vertebrates, Gene, 241, 3. ; Touzet H. (2007), Efficient and accurate P-value computation for Position Weight Matrices, Algorithms for Molecular Biology, 2, doi.org/10.1186/1748-7188-2-15 ; Zhang J. (2007), Computing exact P-values for DNA motifs, Bioinformatics, 23, 531. ; Barash Y. (2003), Modeling dependencies in protein-DNA binding sites, null, 28. ; Zhao X. (2005), Finding short DNA motifs using permuted Markov models, J. Comput. Biol, 12, 894. ; King O. (2003), A non-parametric model for transcription factor binding sites, Nucleic Acids Res, 31, doi.org/10.1093/nar/gng117 ; Lenhard B. (2002), TFBS: Computational framework for transcription factor binding site analysis, Bioinformatics, 18, 1135. ; Hertz G. (1990), Identification of consensus patterns in unaligned DNA sequences known to be functionally related, Comput. Appl. Biosci, 6, 81. ; Kel A. (2003), MATCH: A tool for searching transcription factor binding sites in DNA sequences, Nucleic Acids Res, 31, 3576. ; Loots G. (2004), rVISTA 2.0: evolutionary analysis of transcription factor binding sites, Nucleic Acids Res, 32, doi.org/10.1093/nar/gkh383 ; Marinescu V. (2005), MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes, BMC Bioinformatics, 6, 79. ; Sandelin A. (2004), JASPAR: an open-access database for eukaryotic transcription factor binding profiles, Nucleic Acids Res, 32, doi.org/10.1093/nar/gkh012

Open Access Policy

Archives of Control Sciences is an open access journal with all content available with no charge in full text version.


The journal content is available under the licencse CC BY-NC-ND 4.0 https://creativecommons.org/licenses/by-nc-nd/4.0/.
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