期刊
BIOINFORMATICS
卷 29, 期 9, 页码 1112-1119出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btt096
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类别
资金
- Centre for Genomic Regulation (CRG)
- Spanish Ministerio de Economia y Competitividad through the Plan Nacional [BFU2011-28575]
- Euopean Union [KBBE-2A-222664]
- Fundacio la Caixa
- Department of Pathology at the University of Alabama, Birmingham
- Spanish 60 MINECO [BFU2010-19310]
Motivation: Aligning RNAs is useful to search for homologous genes, study evolutionary relationships, detect conserved regions and identify any patterns that may be of biological relevance. Poor levels of conservation among homologs, however, make it difficult to compare RNA sequences, even when considering closely evolutionary related sequences. Results: We describe SARA-Coffee, a tertiary structure-based multiple RNA aligner, which has been validated using BRAliDARTS, a new benchmark framework designed for evaluating tertiary structure-based multiple RNA aligners. We provide two methods to measure the capacity of alignments to match corresponding secondary and tertiary structure features. On this benchmark, SARA-Coffee outperforms both regular aligners and those using secondary structure information. Furthermore, we show that on sequences in which <60% of the nucleotides form base pairs, primary sequence methods usually perform better than secondary-structure aware aligners.
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