Combinatorial approaches to finding subtle signals in DNA sequences
Affiliations
- PMID: 10977088
Item in Clipboard
Combinatorial approaches to finding subtle signals in DNA sequences
Proc Int Conf Intell Syst Mol Biol.
2000.
Abstract
Signal finding (pattern discovery in unaligned DNA sequences) is a fundamental problem in both computer science and molecular biology with important applications in locating regulatory sites and drug target identification. Despite many studies, this problem is far from being resolved: most signals in DNA sequences are so complicated that we don't yet have good models or reliable algorithms for their recognition. We complement existing statistical and machine learning approaches to this problem by a combinatorial approach that proved to be successful in identifying very subtle signals.
Similar articles
-
An algorithm for finding signals of unknown length in DNA sequences.Bioinformatics. 2001;17 Suppl 1:S207-14. doi: 10.1093/bioinformatics/17.suppl_1.s207. Bioinformatics. 2001. PMID: 11473011
-
Finding subtle motifs with variable gaps in unaligned DNA sequences.Comput Methods Programs Biomed. 2003 Jan;70(1):11-20. doi: 10.1016/s0169-2607(01)00198-5. Comput Methods Programs Biomed. 2003. PMID: 12468123
-
An improved heuristic algorithm for finding motif signals in DNA sequences.IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):959-75. doi: 10.1109/TCBB.2010.92. IEEE/ACM Trans Comput Biol Bioinform. 2011. PMID: 20855921
-
Finding weak motifs in DNA sequences.Pac Symp Biocomput. 2002:235-46. doi: 10.1142/9789812799623_0022. Pac Symp Biocomput. 2002. PMID: 11928479
-
How does DNA sequence motif discovery work?Nat Biotechnol. 2006 Aug;24(8):959-61. doi: 10.1038/nbt0806-959. Nat Biotechnol. 2006. PMID: 16900144 Review. No abstract available.
Cited by
-
qPMS7: a fast algorithm for finding (ℓ, d)-motifs in DNA and protein sequences.PLoS One. 2012;7(7):e41425. doi: 10.1371/journal.pone.0041425. Epub 2012 Jul 24. PLoS One. 2012. PMID: 22848493 Free PMC article.
-
An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.BMC Genomics. 2016 Aug 9;17:578. doi: 10.1186/s12864-016-2982-x. BMC Genomics. 2016. PMID: 27507169 Free PMC article.
-
Improved benchmarks for computational motif discovery.BMC Bioinformatics. 2007 Jun 8;8:193. doi: 10.1186/1471-2105-8-193. BMC Bioinformatics. 2007. PMID: 17559676 Free PMC article.
-
Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites.PLoS Comput Biol. 2007 May;3(5):e90. doi: 10.1371/journal.pcbi.0030090. Epub 2007 Apr 10. PLoS Comput Biol. 2007. PMID: 17500587 Free PMC article.
-
GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery.J Comput Biol. 2009 Feb;16(2):317-29. doi: 10.1089/cmb.2008.16TT. J Comput Biol. 2009. PMID: 19193149 Free PMC article.