Hyppää sisältöön
    • Suomeksi
    • In English
Trepo
  • Suomeksi
  • In English
  • Kirjaudu
Näytä viite 
  •   Etusivu
  • Trepo
  • Artikkelit
  • Näytä viite
  •   Etusivu
  • Trepo
  • Artikkelit
  • Näytä viite
JavaScript is disabled for your browser. Some features of this site may not work without it.

A statistical score for assessing the quality of multiple sequence alignments

Ahola, Virpi; Aittokallio, Tero; Vihinen, Mauno; Uusipaikka, Esa (2006)

 
Avaa tiedosto
a_statistical_score_for_2006.pdf (1.239Mt)
Lataukset: 



Ahola, Virpi
Aittokallio, Tero
Vihinen, Mauno
Uusipaikka, Esa
2006

BMC Bioinformatics 7
484
This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.
doi:10.1186/1471-2105-7-484
Näytä kaikki kuvailutiedot
Julkaisun pysyvä osoite on
https://urn.fi/urn:nbn:uta-3-623

Kuvaus

BioMed Central Open access
Tiivistelmä
Background

Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc. Although the automatic construction of a multiple sequence alignment for a set of remotely related sequences cause a very challenging and error-prone task, many downstream analyses still rely heavily on the accuracy of the alignments.

Results

To address the need for an objective evaluation framework, we introduce a statistical score that assesses the quality of a given multiple sequence alignment. The quality assessment is based on counting the number of significantly conserved positions in the alignment using importance sampling method in conjunction with statistical profile analysis framework. We first evaluate a novel objective function used in the alignment quality score for measuring the positional conservation. The results for the Src homology 2 (SH2) domain, Ras-like proteins, peptidase M13, subtilase and β-lactamase families demonstrate that the score can distinguish sequence patterns with different degrees of conservation. Secondly, we evaluate the quality of the alignments produced by several widely used multiple sequence alignment programs using a novel alignment quality score and a commonly used sum of pairs method. According to these results, the Mafft strategy L-INS-i outperforms the other methods, although the difference between the Probcons, TCoffee and Muscle is mostly insignificant. The novel alignment quality score provides similar results than the sum of pairs method.

Conclusion

The results indicate that the proposed statistical score is useful in assessing the quality of multiple sequence alignments.
Kokoelmat
  • Artikkelit [6122]
Kalevantie 5
PL 617
33014 Tampereen yliopisto
oa[@]tuni.fi | Tietosuoja | Saavutettavuusseloste
 

 

Selaa kokoelmaa

TekijätNimekkeetTiedekunta (2019 -)Tiedekunta (- 2018)Tutkinto-ohjelmat ja opintosuunnatAvainsanatJulkaisuajatKokoelmat

Omat tiedot

Kirjaudu sisäänRekisteröidy
Kalevantie 5
PL 617
33014 Tampereen yliopisto
oa[@]tuni.fi | Tietosuoja | Saavutettavuusseloste