PMID: 8996786Oct 1, 1996Paper

Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case

Computer Applications in the Biosciences : CABIOS
A BolshoyE N Trifonov

Abstract

A nucleosome DNA positioning pattern is known to be one of the weakest (highly degenerated) patterns. The alignment procedure that has been developed recently for the extraction of such a pattern is based on a statistical matching of the sequences, and its success depends on the pattern/background ratio in the individual sequences and in the generated pattern. The heuristic nature of the method and distinctive properties of the pattern bring up the question of efficiency and sensitivity in the procedure. This paper presents a method of verification for this multiple sequence alignment algorithm. To verify the applicability of the multiple alignment approach, we constructed a set of sequences carrying the hidden pattern. The pattern was presented by weak ('signal') oscillations of occurrences of AA and TT dinucleotides along otherwise random sequences. Only a few dinucleotides of any given 145 base long sequence would correspond to the signal, appearing in about the same phase within the simulated periodic pattern. The novelty of our simulation approach is that we simulated a database as a whole, as opposed to simulating each sequence separately. The correlation between the hidden pattern and a sequence from the database is negl...Continue Reading

Citations

Dec 19, 2008·Nature·Noam KaplanEran Segal
Aug 15, 1997·Nucleic Acids Research·A BolshoyI Ioshikhes
Jun 23, 2006·BMC Genomics·Naum I GershenzonIlya P Ioshikhes
Nov 8, 2008·PLoS Computational Biology·Yair FieldEran Segal
Nov 7, 2007·Computational Biology and Chemistry·Alexander Bolshoy
Aug 30, 2008·PLoS Computational Biology·Shobhit GuptaWilliam Stafford Noble
Jan 30, 2008·PLoS Computational Biology·Guo-Cheng Yuan, Jun S Liu
Jun 15, 2010·Forensic Science International. Genetics·Phuvadol Thanakiatkrai, Lindsey Welch
Sep 12, 2006·Nature Genetics·Ilya P IoshikhesB Franklin Pugh

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