Search: onr:"swepub:oai:DiVA.org:uu-148838" >
Identifying novel c...
Identifying novel constrained elements by exploiting biased substitution patterns
- Article/chapterEnglish2009
Publisher, publication year, extent ...
-
2009-05-27
-
Oxford University Press (OUP),2009
-
printrdacarrier
Numbers
-
LIBRIS-ID:oai:DiVA.org:uu-148838
-
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-148838URI
-
https://doi.org/10.1093/bioinformatics/btp190DOI
Supplementary language notes
-
Language:English
-
Summary in:English
Part of subdatabase
Classification
-
Subject category:ref swepub-contenttype
-
Subject category:art swepub-publicationtype
Notes
-
Motivation: Comparing the genomes from closely related species provides a powerful tool to identify functional elements in a reference genome. Many methods have been developed to identify conserved sequences across species; however, existing methods only model conservation as a decrease in the rate of mutation and have ignored selection acting on the pattern of mutations. Results: We present a new approach that takes advantage of deeply sequenced clades to identify evolutionary selection by uncovering not only signatures of rate-based conservation but also substitution patterns characteristic of sequence undergoing natural selection. We describe a new statistical method for modeling biased nucleotide substitutions, a learning algorithm for inferring site-specific substitution biases directly from sequence alignments and a hidden Markov model for detecting constrained elements characterized by biased substitutions. We show that the new approach can identify significantly more degenerate constrained sequences than rate-based methods. Applying it to the ENCODE regions, we identify as much as 10.2% of these regions are under selection.
Subject headings and genre
-
human genome
-
functional elements
-
vertebrate
-
genomes
-
sequence-analysis
-
identification
-
discovery
-
1-percent
-
browser
-
mammals
-
family
-
MEDICINE
-
MEDICIN
Added entries (persons, corporate bodies, meetings, titles ...)
-
Guttman, Mitchell
(author)
-
Clamp, Michele
(author)
-
Zody, Michael C.Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi(Swepub:uu)miczo266
(author)
-
Friedman, Nir
(author)
-
Xie, Xiaohui
(author)
-
Uppsala universitetInstitutionen för medicinsk biokemi och mikrobiologi
(creator_code:org_t)
Related titles
-
In:Bioinformatics: Oxford University Press (OUP)25:12, s. I54-I621367-48031367-4811
Internet link
Find in a library
To the university's database