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Identifying novel c...
Identifying novel constrained elements by exploiting biased substitution patterns
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Garber, Manuel (författare)
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Guttman, Mitchell (författare)
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Clamp, Michele (författare)
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- Zody, Michael C. (författare)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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Friedman, Nir (författare)
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Xie, Xiaohui (författare)
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(creator_code:org_t)
- 2009-05-27
- 2009
- Engelska.
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 25:12, s. I54-I62
- Relaterad länk:
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https://academic.oup...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Nyckelord
- human genome
- functional elements
- vertebrate
- genomes
- sequence-analysis
- identification
- discovery
- 1-percent
- browser
- mammals
- family
- MEDICINE
- MEDICIN
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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