Consiglio Nazionale delle Ricerche

Tipo di prodottoContributo in atti di convegno
TitoloJoint correction of cross-talk and peak spreading in DNA electropherograms
Anno di pubblicazione2006
FormatoElettronico
Autore/iTonazzini A., Bedini L.
Affiliazioni autoriCNR-ISTI, Pisa, Italy; CNR-ISTI, Pisa, Italy;
Autori CNR e affiliazioni
  • ANNA TONAZZINI
Lingua/e
  • inglese
AbstractIn automated DNA sequencing, the final algorithmic phase, referred to as basecalling, consists of the translation of four time signals in the form of peak sequences (electropherogram) to the corresponding sequence of bases. The most popular basecaller, Phred, detects the peaks based on heuristics, and is very efficient when the peaks are well distinct and quite regular in spread, amplitude and spacing. Unfortunately, in the practice the data is subject to several degradations, particularly near the end of the sequence. The most frequent ones are peak superposition, peak merging and signal leakage, resulting in secondary peaks. In these conditions the experiment must be repeated and the human intervention is required. Recently, there have been attempts to provide methodological foundations to the problem and use statistical models to solve it. In this paper, we propose exploiting a priori information and Bayesian estimation to remove degradations and recover the signals in an impulsive form which makes the task of basecalling straightforward.
Lingua abstractinglese
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Pagine totali2
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Verificato da refereeSì: Internazionale
Stato della pubblicazionePublished version
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Parole chiaveDNA sequencing, Basecalling, Blind source separation, Blind deconvolution
Link (URL, URI)-
Titolo convegno/congressoRECOMB 2006. The 10th Annual International Conference on Research in Computational Molecular Biology
Luogo convegno/congressoVenice
Data/e convegno/congresso01-04/04/2006
RilevanzaInternazionale
RelazioneContributo
Titolo parallelo-
Note/Altre informazioniCodice Puma: cnr.isti/2006-A2-34
Strutture CNR
  • ISTI — Istituto di scienza e tecnologie dell'informazione "Alessandro Faedo"
Moduli/Attività/Sottoprogetti CNR
  • INT.P02.003.004 : Modelli, metodi ed algoritmi per l'analisi di dati genomici e e di processi biologici
Progetti Europei-
Allegati
Joint correction of cross-talk and peak spreading in DNA electropherograms (documento privato )
Tipo documento: application/pdf

Dati storici
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Area disciplinareComputer Science & Engineering
NoteIn: RECOMB 2006. The 10th Annual International Conference on Research in Computational Molecular Biology (Venice, 1-4 April 2006). Proceedings, pp. 2-. 2006.
Descrizione sintetica del prodottoABSTRACT: In automated DNA sequencing, the final algorithmic phase, referred to as basecalling, consists of the translation of four time signals in the form of peak sequences (electropherogram) to the corresponding sequence of bases. The most popular basecaller, Phred, detects the peaks based on heuristics, and is very efficient when the peaks are well distinct and quite regular in spread, amplitude and spacing. Unfortunately, in the practice the data is subject to several degradations, particularly near the end of the sequence. The most frequent ones are peak superposition, peak merging and signal leakage, resulting in secondary peaks. In these conditions the experiment must be repeated and the human intervention is required. Recently, there have been attempts to provide methodological foundations to the problem and use statistical models to solve it. In this paper, we propose exploiting a priori information and Bayesian estimation to remove degradations and recover the signals in an impulsive form which makes the task of basecalling straightforward.