IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v3y2004i1n28.html
   My bibliography  Save this article

Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment

Author

Listed:
  • Ahola Virpi

    (University of Turku)

  • Aittokallio Tero

    (University of Turku)

  • Uusipaikka Esa

    (University of Turku)

  • Vihinen Mauno

    (University of Tampere)

Abstract

The assessment of residue conservation in a multiple sequence alignment is a central issue in bioinformatics. Conserved residues and regions are used to determine structural and functional motifs or evolutionary relationships between the sequences of a multiple sequence alignment. For this reason, residue conservation is a valuable measure for database and motif search or for estimating the quality of alignments. In this paper, we present statistical methods for identifying conserved residues in multiple sequence alignments. While most earlier studies examine the positional conservation of the alignment, we focus on the detection of individual conserved residues at a position. The major advantages of multiple comparison methods originate from their ability to select conserved residues simultaneously and to consider the variability of the residue estimates. Large-scale simulations were used for the comparative analysis of the methods. Practical performance was studied by comparing the structurally and functionally important residues of Src homology 2 (SH2) domains to the assignments of the conservation indices. The applicability of the indices was also compared in three additional protein families comprising different degrees of entropy and variability in alignment positions. The results indicate that statistical multiple comparison methods are sensitive and reliable in identifying conserved residues.

Suggested Citation

  • Ahola Virpi & Aittokallio Tero & Uusipaikka Esa & Vihinen Mauno, 2004. "Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-30, October.
  • Handle: RePEc:bpj:sagmbi:v:3:y:2004:i:1:n:28
    DOI: 10.2202/1544-6115.1074
    as

    Download full text from publisher

    File URL: https://doi.org/10.2202/1544-6115.1074
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.

    File URL: https://libkey.io/10.2202/1544-6115.1074?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Selby, Ashley & Petäjistö, Leena & Huhtala, Maija, 2011. "The realisation of tourism business opportunities adjacent to three national parks in southern Finland: entrepreneurs and local decision-makers matter," Forest Policy and Economics, Elsevier, vol. 13(6), pages 446-455, July.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bpj:sagmbi:v:3:y:2004:i:1:n:28. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.