Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (278K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (44)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Grillo, G.
Right arrow Articles by Pesole, G.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Grillo, G.
Right arrow Articles by Pesole, G.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 13 3608-3612
© 2003 Oxford University Press

PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences

Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà and Graziano Pesole*,1

Sezione di Bioinformatica e Genomica di Bari, Istituto Tecnologie Biomediche CNR, via Amendola 168/5, 70125 Bari, Italy 1 Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, via Celoria 26, 20133 Milano, Italy

*To whom correspondence should be addressed. Tel: +39 02 50314915; Fax: +39 02 50314912; Email: graziano.pesole{at}unimi.it

Regulation of gene expression at transcriptional and post-transcriptional level involves the interaction between short DNA or RNA tracts and the corresponding trans-acting protein factors. Detection of such cis-acting elements in genome-wide screenings may significantly contribute to genome annotation and comparative analysis as well as to target functional characterization experiments. We present here PatSearch, a flexible and fast pattern matcher able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices. It can also allow for mismatches/mispairings below a user fixed threshold. We report three different applications of the program in the search of complex patterns such as those of the iron responsive element hairpin-loop structure, the p53 responsive element and a promoter module containing CAAT-, TATA- and cap-boxes. PatSearch is available on the web at http://bighost.area.ba.cnr.it/BIG/PatSearch/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
G. Grillo, A. Turi, F. Licciulli, F. Mignone, S. Liuni, S. Banfi, V. A. Gennarino, D. S. Horner, G. Pavesi, E. Picardi, et al.
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
Nucleic Acids Res., October 30, 2009; (2009) gkp902v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Brazdova, T. Quante, L. Togel, K. Walter, C. Loscher, V. Tichy, L. Cincarova, W. Deppert, and G. V. Tolstonog
Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 R273H to intronic and intergenic sequences
Nucleic Acids Res., April 1, 2009; 37(5): 1486 - 1500.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Li, E. S. Ho, S. I. Gunderson, and M. Kiledjian
Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5'-end stem-loop structures
Nucleic Acids Res., April 1, 2009; 37(7): 2227 - 2237.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
F. Silvestris, P. Cafforio, M. De Matteo, N. Calvani, M. A. Frassanito, and F. Dammacco
Negative Regulation of the Osteoblast Function in Multiple Myeloma through the Repressor Gene E4BP4 Activated by Malignant Plasma Cells
Clin. Cancer Res., October 1, 2008; 14(19): 6081 - 6091.
[Abstract] [Full Text] [PDF]

Home page
 EndocrinologyHome page
X. Rui, J. Tsao, J. O. Scheys, G. D. Hammer, and B. P. Schimmer
Contributions of Specificity Protein-1 and Steroidogenic Factor 1 to Adcy4 Expression in Y1 Mouse Adrenal Cells
Endocrinology, July 1, 2008; 149(7): 3668 - 3678.
[Abstract] [Full Text] [PDF]

Home page
 DevelopmentHome page
N. Lo Iacono, S. Mantero, A. Chiarelli, E. Garcia, A. A. Mills, M. I. Morasso, A. Costanzo, G. Levi, L. Guerrini, and G. R. Merlo
Regulation of Dlx5 and Dlx6 gene expression by p63 is involved in EEC and SHFM congenital limb defects
Development, April 1, 2008; 135(7): 1377 - 1388.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
K. Chakrabarti, M. Pearson, L. Grate, T. Sterne-Weiler, J. Deans, J. P. Donohue, and M. Ares Jr
Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis
RNA, November 1, 2007; 13(11): 1923 - 1939.
[Abstract] [Full Text] [PDF]

Home page
 JCBHome page
B. Culjkovic, I. Topisirovic, L. Skrabanek, M. Ruiz-Gutierrez, and K. L.B. Borden
eIF4E is a central node of an RNA regulon that governs cellular proliferation
J. Cell Biol., November 6, 2006; 175(3): 415 - 426.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
S. D. Baird, M. Turcotte, R. G. Korneluk, and M. Holcik
Searching for IRES
RNA, October 1, 2006; 12(10): 1755 - 1785.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T.-H. Chang, H.-D. Huang, T.-N. Chuang, D.-M. Shien, and J.-T. Horng
RNAMST: efficient and flexible approach for identifying RNA structural homologs.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W423 - W428.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H.-Y. Huang, C.-H. Chien, K.-H. Jen, and H.-D. Huang
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W429 - W434.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
K. Walter, G. Warnecke, R. Bowater, W. Deppert, and E. Kim
Tumor Suppressor p53 Binds with High Affinity to CTG{middle dot}CAG Trinucleotide Repeats and Induces Topological Alterations in Mismatched Duplexes
J. Biol. Chem., December 30, 2005; 280(52): 42497 - 42507.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Yan, D. Yoo, T. Z. Berardini, L. A. Mueller, D. C. Weems, S. Weng, J. M. Cherry, and S. Y. Rhee
PatMatch: a program for finding patterns in peptide and nucleotide sequences
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W262 - W266.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Mignone, G. Grillo, F. Licciulli, M. Iacono, S. Liuni, P. J. Kersey, J. Duarte, C. Saccone, and G. Pesole
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D141 - D146.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Pavesi, G. Mauri, M. Stefani, and G. Pesole
RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
Nucleic Acids Res., June 15, 2004; 32(10): 3258 - 3269.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
Y. HATAKEYAMA, N. SHIBUYA, T. NISHIYAMA, and N. NAKASHIMA
Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts
RNA, May 1, 2004; 10(5): 779 - 786.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.