De novo prediction of structured RNAs from genomic sequences

Jan Gorodkin; Ivo L. Hofacker; Elfar Þórarinsson; Zizhen Yao; Jakob Hull Havgaard; Walter L. Ruzzo

doi:10.1016/j.tibtech.2009.09.006

De novo prediction of structured RNAs from genomic sequences

Jan Gorodkin, Ivo L. Hofacker, Elfar Þórarinsson, Zizhen Yao, Jakob Hull Havgaard, Walter L. Ruzzo

55 Citationer (Scopus)

Abstract

Growing recognition of the numerous, diverse and important roles played by non-coding RNA in all organisms motivates better elucidation of these cellular components. Comparative genomics is a powerful tool for this task and is arguably preferable to any high-throughput experimental technology currently available, because evolutionary conservation highlights functionally important regions. Conserved secondary structure, rather than primary sequence, is the hallmark of many functionally important RNAs, because compensatory substitutions in base-paired regions preserve structure. Unfortunately, such substitutions also obscure sequence identity and confound alignment algorithms, which complicates analysis greatly. This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist

Originalsprog	Engelsk
Tidsskrift	Trends in Biotechnology
Vol/bind	28
Udgave nummer	1
Sider (fra-til)	9-19
Antal sider	11
ISSN	0167-7799
DOI	https://doi.org/10.1016/j.tibtech.2009.09.006
Status	Udgivet - jan. 2010

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10.1016/j.tibtech.2009.09.006

Citationsformater

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AU - Gorodkin, Jan

AU - Hofacker, Ivo L.

AU - Þórarinsson, Elfar

AU - Yao, Zizhen

AU - Havgaard, Jakob Hull

AU - Ruzzo, Walter L.

PY - 2010/1

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N2 - Growing recognition of the numerous, diverse and important roles played by non-coding RNA in all organisms motivates better elucidation of these cellular components. Comparative genomics is a powerful tool for this task and is arguably preferable to any high-throughput experimental technology currently available, because evolutionary conservation highlights functionally important regions. Conserved secondary structure, rather than primary sequence, is the hallmark of many functionally important RNAs, because compensatory substitutions in base-paired regions preserve structure. Unfortunately, such substitutions also obscure sequence identity and confound alignment algorithms, which complicates analysis greatly. This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist

AB - Growing recognition of the numerous, diverse and important roles played by non-coding RNA in all organisms motivates better elucidation of these cellular components. Comparative genomics is a powerful tool for this task and is arguably preferable to any high-throughput experimental technology currently available, because evolutionary conservation highlights functionally important regions. Conserved secondary structure, rather than primary sequence, is the hallmark of many functionally important RNAs, because compensatory substitutions in base-paired regions preserve structure. Unfortunately, such substitutions also obscure sequence identity and confound alignment algorithms, which complicates analysis greatly. This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist

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DO - 10.1016/j.tibtech.2009.09.006

M3 - Journal article

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JO - Trends in Biotechnology

JF - Trends in Biotechnology

IS - 1

ER -

De novo prediction of structured RNAs from genomic sequences

Abstract

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