Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Motif Yggdrasil: Sampling from a tree mixture model
KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
2006 (English)In: Research In Computational Molecular Biology, Proceedings / [ed] Apostolico, A; Guerra, C; Istrail, S; Pevzner, P; Waterman, M, 2006, Vol. 3909, 458-472 p.Conference paper, Published paper (Refereed)
Abstract [en]

In phylogenetic foot-printing, putative regulatory elements are found in upstream regions of orthologous genes by searching for common motifs. Motifs in different upstream sequences are subject to mutations along the edges of the corresponding phylogenetic tree, consequently taking advantage of the tree in the motif search is an appealing idea. We describe the Motif Yggdrasil sampler; the first Gibbs sampler based on a general tree that uses unaligned sequences. Previous tree-based Gibbs samplers have assumed a star-shaped tree or partially aligned upstream regions. We give a probabilistic model describing upstream sequences with regulatory elements and build a Gibbs sampler with respect to this model. We apply the collapsing technique to eliminate the need to sample nuisance parameters, and give a derivation of the predictive update formula. The use of the tree achieves a substantial increase in nucleotide level correlation coefficient both for synthetic data and 37 bacterial lexA genes.

Place, publisher, year, edition, pages
2006. Vol. 3909, 458-472 p.
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 3909
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-42028DOI: 10.1007/11732990_39ISI: 000236991800039Scopus ID: 2-s2.0-33745769012ISBN: 3-540-33295-2 (print)OAI: oai:DiVA.org:kth-42028DiVA: diva2:446077
Conference
10th Annual International Conference on Research in Computational Molecular Biology Location: Venice, Italy, Date: APR 02-05, 2006
Note
QC 20111006Available from: 2011-10-06 Created: 2011-10-05 Last updated: 2011-10-06Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textScopus

Search in DiVA

By author/editor
Andersson, Samuel A.Lagergren, Jens
By organisation
Numerical Analysis and Computer Science, NADA
Bioinformatics (Computational Biology)

Search outside of DiVA

GoogleGoogle Scholar

doi
isbn
urn-nbn

Altmetric score

doi
isbn
urn-nbn
Total: 57 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf