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Sökning: WFRF:(Friedman Nir) > (2009) > Identifying novel c...
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| Fältnamn | Indikatorer | Metadata |
|---|---|---|
| 000 | 02930naa a2200493 4500 | |
| 001 | oai:DiVA.org:uu-148838 | |
| 003 | SwePub | |
| 008 | 110310s2009 | |||||||||||000 ||eng| | |
| 024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1488382 URI |
| 024 | 7 | a https://doi.org/10.1093/bioinformatics/btp1902 DOI |
| 040 | a (SwePub)uu | |
| 041 | a engb eng | |
| 042 | 9 SwePub | |
| 072 | 7 | a ref2 swepub-contenttype |
| 072 | 7 | a art2 swepub-publicationtype |
| 100 | 1 | a Garber, Manuel4 aut |
| 245 | 1 0 | a Identifying novel constrained elements by exploiting biased substitution patterns |
| 264 | c 2009-05-27 | |
| 264 | 1 | b Oxford University Press (OUP),c 2009 |
| 338 | a print2 rdacarrier | |
| 520 | a 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. | |
| 653 | a human genome | |
| 653 | a functional elements | |
| 653 | a vertebrate | |
| 653 | a genomes | |
| 653 | a sequence-analysis | |
| 653 | a identification | |
| 653 | a discovery | |
| 653 | a 1-percent | |
| 653 | a browser | |
| 653 | a mammals | |
| 653 | a family | |
| 653 | a MEDICINE | |
| 653 | a MEDICIN | |
| 700 | 1 | a Guttman, Mitchell4 aut |
| 700 | 1 | a Clamp, Michele4 aut |
| 700 | 1 | a Zody, Michael C.u Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi4 aut0 (Swepub:uu)miczo266 |
| 700 | 1 | a Friedman, Nir4 aut |
| 700 | 1 | a Xie, Xiaohui4 aut |
| 710 | 2 | a Uppsala universitetb Institutionen för medicinsk biokemi och mikrobiologi4 org |
| 773 | 0 | t Bioinformaticsd : Oxford University Press (OUP)g 25:12, s. I54-I62q 25:12<I54-I62x 1367-4803x 1367-4811 |
| 856 | 4 | u https://academic.oup.com/bioinformatics/article-pdf/25/12/i54/16887420/btp190.pdf |
| 856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-148838 |
| 856 | 4 8 | u https://doi.org/10.1093/bioinformatics/btp190 |
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