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*  Promoter Regions, Genetic | Colorado PROFILES
Base Sequence [G02.111.570.080]. *Regulatory Sequences, Nucleic Acid [G02.111.570.080.689]. *Promoter Regions, Genetic [G02.111 ... Regulatory Elements, Transcriptional [G05.360.340.024.340.137.750]. *Promoter Regions, Genetic [G05.360.340.024.340.137.750.680 ... DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation ... Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes. ...
https://profiles.ucdenver.edu/display/219535
*  Algorithms accessible via Chinook - Canada's Michael Smith Genome Sciences Centre
Regulatory sequence analysis tools. Nucleic Acids Res 31: 3593-3596. (*)STUBB Sinha, S., E. Van Nimwegen, and E.D. Siggia. 2003 ... Nucleic Acids Res. 22(22):4673-80. (*)Conreal Berezikov, E., V. Guryev, R.H. Plasterk, and E. Cuppen. 2004. CONREAL: conserved ... Nucleic Acids Res. 2003 Jul 1;31(13):3580-5. MEME Bailey TL, and C. Elkan. 1994. Fitting a mixture model by expectation ... CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific ...
http://www.bcgsc.ca/project/bomge/chinook/algorithms
*  Algorithms currently supported by the Sockeye Platform (through Chinook) - Canada's Michael Smith Genome Sciences Centre
Regulatory sequence analysis tools. Nucleic Acids Res 31: 3593-3596. (*)STUBB Sinha, S., E. Van Nimwegen, and E.D. Siggia. 2003 ... Nucleic Acids Res. 22(22):4673-80. (*)Conreal Berezikov, E., V. Guryev, R.H. Plasterk, and E. Cuppen. 2004. CONREAL: conserved ... Nucleic Acids Res. 2003 Jul 1;31(13):3580-5. MEME Bailey TL, and C. Elkan. 1994. Fitting a mixture model by expectation ... Multi-species Conserved Sequences. MCS Analysis E.H. Margulies, M. Blanchette, NISC Comparative Sequencing Program, D. Haussler ...
http://www.bcgsc.ca/project/bomge/sockeye/algorithms
*  Frontiers | Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune...
Comparison within the human and mouse sequences showed less than 1% sequence conservation although we identified multiple ... Comparison within the human and mouse sequences showed less than 1% sequence conservation although we identified multiple ... These lncRNAs are predominantly cell-type specific, composed of large regions of repeat sequences and show poor evolutionary ... These lncRNAs are predominantly cell-type specific, composed of large regions of repeat sequences and show poor evolutionary ...
https://www.frontiersin.org/articles/10.3389/fimmu.2017.01038/full
*  Plus it
2005) TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res 33:W393-W396. ... Consistent with a regulatory role of AKT on NSPC proliferation, we found 14 and 17% increase in the number of BrdU+ and p-H3+ ... DNA sequences for SH2B3 (LNK) corresponding to conserved regions between the human, mouse, rat, horse, and dog species upstream ... The regulatory element of mouse Lnk where we detected STAT1 binding, 2000 bp upstream and 300 bp downstream of the predicted ...
http://www.jneurosci.org/content/32/15/5151
*  Multiplexed analysis of chromosome conformation at vastly improved sensitivity. - Radcliffe Department of Medicine
Chromosomes, Human, Humans, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, Reproducibility of Results ...
https://www.rdm.ox.ac.uk/publications/579451
*  Bioinformatic Methods to Discover Cis-regulatory Elements in mRNAs | SpringerLink
Cis-regulatory elements play a number of important roles in determining the fate of messenger RNAs (mRNAs). Due to these ... A database to aid the analysis of regulatory sequences in mRNAs, Nucleic Acids Res. 37, D72-76 (2009)CrossRefGoogle Scholar ... A collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs, Nucleic Acids Res. 38, D75-80 ... T.L. Bailey, N. Williams, C. Misleh, W.W. Li: MEME: Discovering and analyzing DNA and protein sequence motifs, Nucleic Acids ...
https://link.springer.com/chapter/10.1007%2F978-3-642-30574-0_10
*  Transcriptomic Analysis Reveals Calcium Regulation of Specific Promoter Motifs in Arabidopsis | Plant Cell
2003). Regulatory sequence analysis tools. Nucleic Acids Res. 31: 3593-3596.. OpenUrlAbstract/FREE Full Text ... also revealed sequences that we identified as previously described cis-regulatory elements. The sequence ACCGACAT (Figure 2C) ... 1989). Abscisic acid-responsive sequences from the Em gene of wheat. Plant Cell 1: 969-976. ... Supplemental Figure 1. RSAT Alignments of Hexamer Sequences Relating to the ABRE and CAM Box cis-Element Sequences. ...
http://www.plantcell.org/content/23/11/4079?ijkey=0a229247ea66ef8626678be936234a7c6a644dc2&keytype2=tf_ipsecsha
*  JCI Insight - MED12 regulates a transcriptional network of calcium-handling genes in the heart
RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Res. 2015;43(W1):W50-W56.. View this article via: PubMed CrossRef ... Identifying synonymous regulatory elements in vertebrate genomes. Nucleic Acids Res. 2005;33(Web Server issue):W403-W407.. View ... Nucleic Acids Res. 2007;35(Web Server issue):W169-W175.. View this article via: PubMed Google Scholar ... De novo motif discovery in MEF2 ChIP-seq peak regions were identified using Regulatory Sequence Analysis Tools (RSAT) (34). ...
https://insight.jci.org/articles/view/91920
*  Информация о публикации | Институт вычислительных технологий СО РАН
2015) RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Res., 43, W50-W56. 15. Zhang, Y., Liu, T., Meyer, C. A., ... Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models. Nucleic Acids Res, 42, ... Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. Nucleic Acids Res., 44, 6055- ... Nucleic Acids Res., 45, D61-D67. 20. Kulakovskiy, I. V, Vorontsov, I. E., Yevshin, I. S., Soboleva, A. V, Kasianov, A. S., ...
http://www.ict.nsc.ru/ru/structure/persons/informaciya-o-publikacii?id=60831
*  Systematic Identification, Evolution and Expression Analysis of the Zea mays PHT1 Gene Family Reveals Several New Members...
RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Res. 2015;43:W50-W56. doi: 10.1093/nar/gkv362. [PMC free article] ... Nucleic Acids Res. 2012;40:D1178-D1186. doi: 10.1093/nar/gkr944. [PMC free article] [PubMed] [Cross Ref] ... Nucleic Acids Res. 2015;43:D662-D669. doi: 10.1093/nar/gku1010. [PMC free article] [PubMed] [Cross Ref] ... Nucleic Acids Res. 2009;37:W202-W208. doi: 10.1093/nar/gkp335. [PMC free article] [PubMed] [Cross Ref] ...
http://pubmedcentralcanada.ca/pmcc/articles/PMC4926463/
*  Composability of regulatory sequences controlling transcription and translation in Escherichia coli | PNAS
Nucleic Acids Res 22(7):1287-1295.. OpenUrlAbstract/FREE Full Text ... 2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad ... Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Sriram Kosuri, Daniel B. ... Composability of regulatory sequences controlling transcription and translation in Escherichia coli Message Subject (Your Name ...
https://www.pnas.org/content/110/34/14024?ijkey=cffd197dee4081b0b8a13a2e150a0487c9e9bdbb&keytype2=tf_ipsecsha
*  Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces...
van Helden J: Regulatory sequence analysis tools. Nucleic Acids Research. 2003, 31 (13): 3593-3596. 10.1093/nar/gkg567. ... upstream from the start codon using the collection of software tools provided by the web resource Regulatory Sequence Analysis ... a shorter sequence is retrieved to discard coding sequences.. We now give a brief description of the 585 variables (see also ... The p variables reflect properties of the occurrences of the GATA motif in the upstream non-coding sequences of the yeast genes ...
https://rd.springer.com/article/10.1186/1753-6561-2-s4-s5
*  Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks | Springer for...
Background The learning of global genetic regulatory networks from expression data is a severely under-constrained problem that ... van Helden Jacques: Regulatory sequence analysis tools. Nucleic Acids Res 2003, 31(13):3593-3596.PubMedCentralCrossRefPubMed ... Schneider TD, Stephens RM: Sequence logos: A new way to display consensus sequences. Nucleic Acids Res 1990, 18: 6097-6100. [ ... Upstream sequences. Upstream sequences for all organisms were obtained from GenBank using the Regulatory Sequence Analysis ...
https://rd.springer.com/article/10.1186/1471-2105-7-280
*  The Arabidopsis Mediator Complex Subunits MED16, MED14, and MED2 Regulate Mediator and RNA Polymerase II Recruitment to CBF...
2011). RSAT 2011: Regulatory sequence analysis tools. Nucleic Acids Res. 39 (Web Server issue): W86-W91. ... to provide a graphical representation of the nucleic acid multiple sequence alignments. All settings were default except for ... Consensus sequences for the two most significantly enriched sequences within promoters of the 81 cold-upregulated genes showing ... jasmonic acid. Col-0. Columbia-0. ChIP. chromatin immunoprecipitation. CaMV. cauliflower mosaic virus. AcH3. acetylated Histone ...
http://www.plantcell.org/content/26/1/465.full
*  US6344323B1 - Compositions and methods for inhibiting cox-2 expression and treating cox-2 associated disorders by using cox-2...
... sequence and the nucleic acid regulated by the regulatory sequence. The operably linked regulatory sequence controls the ... As used herein, the term "nucleic acid," "polynucleotide," "oligonucleotide" or "nucleic acid sequence" refers to a polymer of ... Oligonucleotide or nucleic acid sequences of the invention include DNA, RNA, and cDNA sequences. ... The target includes sequences upstream from the 5′ terminus of the structural gene, such as regulatory sequences, and sequences ...
https://patents.google.com/patent/US6344323
*  Muteins of the c5a anaphylatoxin, nucleic acid molecules encoding such muteins, and pharmaceutical uses of muteins of the c5a...
... to nucleic acid molecules comprising a nucleotide sequence encoding such muteins of C5a anaph ... besides the above-mentioned regulatory sequences and a nucleic acid sequence which codes for a nucleic acid sequence coding for ... A nucleic acid molecule of claim 22, wherein the regulatory sequence comprises a promoter sequence. 24. The nucleic acid ... A nucleic acid molecule of claim 20 or 21, wherein the nucleic acid molecule is operably linked to a regulatory sequence to ...
http://www.freepatentsonline.com/y2006/0052294.html
*  US6884619B2 - Inhibition of BEHAB cleavage and primary central nervous system (CNS) tumors - Google Patents
... nucleic acid sequence comprising a nucleic acid which encodes a promoter/regulatory sequence operably linked to nucleic acid ... 6. The isolated nucleic acid of claim 1. , said nucleic acid further comprising a nucleic acid specifying a promoter/regulatory ... The isolated nucleic acid of claim 11. , wherein said nucleic acid is at least about 99.8% complementary to the nucleic acid ... 4. The isolated nucleic acid of claim 1. , said nucleic acid further comprising a nucleic acid encoding a tag polypeptide ...
https://patents.google.com/patent/US6884619
*  Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation | BMC Plant Biology | Full Text
In Arabidopsis, isochorismate synthase encoded by SID2 is essential for the biosynthesis of salicylic acid in response to ... mobility shift assay CBP60g and SARD1 were shown to bind specifically to a 10mer oligonucleotide with the sequence GAAATTTTGG. ... Salicylic acid is a critical signalling component in plant defence responses. ... van Helden J: Regulatory sequence analysis tools. Nucleic Acids Res. 2003, 31: 3593-3596.PubMedPubMed CentralView ArticleGoogle ...
https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-216
*  Surrogate Genetics in the Frog Oocyte | SpringerLink
Their idea that a single regulatory sequence, the operon, controlled and co-ordinated the expression of several structural... ... A regulatory sequence near the 3′ end of sea urchin histone genes. Nucleic Acids Res., 9, 2997.CrossRefGoogle Scholar ... The leader sequences of simian virus 40 mRNA are not transcribed adjacent to the coding sequences. Proc. Natl. Acad. Sci. USA, ... Their idea that a single regulatory sequence, the operon, controlled and co-ordinated the expression of several structural ...
https://link.springer.com/chapter/10.1007/978-1-4684-3707-2_17
*  MATLIGN: a motif clustering, comparison and matching tool | BMC Bioinformatics | Full Text
Matlign is a user-friendly tool for post-processing large collections of DNA sequence motifs. Starting from a large number of ... Our analyses show that Matlign can reliably discover the most similar analogue from a collection of characterised regulatory ... The computational identification of over-represented motifs in sets of DNA sequences is, in particular, a task where post- ... or degenerate consensus sequences (CS). These formats are used to represent the characterised TFBS profiles stored in ...
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-189
*  Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks | BMC...
... integrating the biclustering of gene expression data and various functional associations with the de novo detection of sequence ... One important association is the presence of one or more common cis-regulatory motifs. In organisms where these motifs are not ... We have applied this procedure to the archaeon Halobacterium NRC-1, as part of our efforts to decipher its regulatory network. ... The learning of global genetic regulatory networks from expression data is a severely under-constrained problem that is aided ...
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-280
*  Publications | Max Planck Institute for Biophysical Chemistry
The BaMM web server for de-novo motif discovery and regulatory sequence analysis. Nucleic Acids Research 46 (W1), pp. W215 - ... Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Research 45 (D1), pp. D170 ... The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids ... Steinegger, M.; Söding, J.: MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature ...
https://www.mpibpc.mpg.de/soeding/publications
*  Regulatory effects of cAMP receptor protein (CRP) on porin genes and its own gene in Yersinia pestis | BMC Microbiology | Full...
Although the CRP of Y. pestis shows a very high homology to that of E. coli, and the consensus DNA sequence recognized by CRP ... No transcriptional regulatory association between CRP and its own gene can be detected in Y. pestis, which is also in contrast ... Y. pestis employs a distinct mechanism indicating that CRP has no regulatory effect on the ompR-envZ operon; however, it ... which is different from the relevant regulatory circuit of E. coli. Data presented here indicate a remarkable remodeling of the ...
https://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-11-40
*  Publikationen | Max-Planck-Institut für biophysikalische Chemie
The BaMM web server for de-novo motif discovery and regulatory sequence analysis. Nucleic Acids Research 46 (W1), S. W215 - ... Liepe, J.; Ovaa, H.; Mishto, M.: Why do proteases mess up with antigen presentation by re-shuffling antigen sequences? Current ... Steinegger, M.; Söding, J.: Clustering huge protein sequence sets in linear time. Nature Communications (2018) ... HLA-G mediated immune regulation is impaired by a single amino acid exchange in the alpha 2 domain. Human Immunology 79 (6), S ...
http://www.mpibpc.mpg.de/publikationen