Grillo Giorgio, Giorgio and Licciulli, Flavio and Liuni, Sabino and Sbisà, Elisabetta and Pesole, Graziano (2003) PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Research, 31 (13). pp. 3608-3612. ISSN 1362-4962
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Abstract
Regulation of gene expression at transcriptional and post-transcriptional level involves the interaction between short DNA or RNA tracts and the corre- sponding trans-acting protein factors. Detection of such cis-acting elements in genome-wide screen- ings may significantly contribute to genome annota- tion 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 oligonu- cleotide 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 applica- tions 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/.
| Item Type: | Article |
|---|---|
| Subjects: | 500 Scienze naturali e Matematica > 570 Scienze della vita; Biologia |
| Depositing User: | Sabino SL Liuni |
| Date Deposited: | 21 Dec 2016 13:31 |
| Last Modified: | 21 Dec 2016 13:31 |
| URI: | http://eprints.bice.rm.cnr.it/id/eprint/15450 |
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