A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage (Articolo in rivista)

Type

• Prodotto della ricerca (Classe)
• Articolo in rivista (Classe)

Label

• A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage (Articolo in rivista) (literal)

Anno

• 2007-01-01T00:00:00+01:00 (literal)

Alternative label

• [1] Genovese L. M., [1] Geraci F., [1] Pellegrini M. (2007)
  A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage
  in Lecture notes in computer science; Springer, Berlin (Germania)
  (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori

• [1] Genovese L. M., [1] Geraci F., [1] Pellegrini M. (literal)

Pagina inizio

• 49 (literal)

Pagina fine

• 60 (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#altreInformazioni

• Codice originale: /cnr.iit/2007-A0-019 (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume

• 4645 (literal)

Rivista

• Lecture notes in computer science (Rivista)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#note

• Proceeding of 7th Workshop on Algorithms in Bioinformatics (WABI'07), Philadelphia, USA, September 2007 (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#pagineTotali

• 12 (literal)

Note

• Scopu (literal)
• ISI Web of Science (WOS) (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni

• [1] IIT-CNR, Pisa, Italy (literal)

Titolo

• A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage (literal)

Abstract

• Single nucleotide polymorphism (SNP) is the most frequent form of DNA variation. The set of SNPs present in a chromosome (called the haplotype) is of interest in a wide area of applications in molecular biology and biomedicine, including diagnostic and medical therapy. In this paper we propose a new heuristic method for the problem of haplotype reconstruction for (portions of ) a pair of homologous human chromosomes from a single individual (SIH). The problem is well known in literature and exact algorithms have been proposed for the case when no (or few) gaps are allowed in the input fragments. These algorithms, though exact and of polynomial complexity, are slow in practice. Therefore fast heuristics have been proposed. In this paper we describe a new heuristic method that is able to tackle the case of many gapped fragments and retains its effectiveness even when the input fragments have high rate of reading errors (up to 20%) and low coverage (as low as 3). We test our method on real data from the HapMap Project. (literal)

Editore

• Springer (Editore)

Prodotto di

• Metodi e algoritmi efficienti per la risoluzione di problemi complessi (ICT.P11.011.001) (Modulo)
• Istituto di informatica e telematica (IIT) (Istituto)
• Algoritmica per bioinformatica (INT.P02.003.003) (Modulo)

Autore CNR

• LOREDANA GENOVESE (Persona)
• FILIPPO GERACI (Unità di personale esterno)
• MARCO PELLEGRINI (Unità di personale interno)

Insieme di parole chiave

• Keywords of "A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage" (Insieme di parole chiave)

Incoming links:

Prodotto

• Istituto di informatica e telematica (IIT) (Istituto)
• Metodi e algoritmi efficienti per la risoluzione di problemi complessi (ICT.P11.011.001) (Modulo)
• Algoritmica per bioinformatica (INT.P02.003.003) (Modulo)

Autore CNR di

• MARCO PELLEGRINI (Unità di personale interno)
• FILIPPO GERACI (Unità di personale esterno)
• LOREDANA GENOVESE (Persona)

Editore di

• Springer (Editore)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#rivistaDi

• Lecture notes in computer science (Rivista)

Insieme di parole chiave di

• Keywords of "A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage" (Insieme di parole chiave)