Journal
BIOINFORMATICS
Volume 32, Issue 8, Pages 1238-1240Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btv748
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Funding
- Innovationfund Denmark
- Danish Research Council for independent research (FTP)
- Lundbeck foundation
- Danish Center for Scientific Computing (DCSC, DeiC)
- CAPES Foundation, Ministry of Education of Brazil, Brasilia - DF [99999.005168/2014-07]
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Motivation: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus, the need for tools which in particular can make local structural alignments of RNAs is only increasing. Results: To meet the demand for both large-scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign. We substantially improve execution time while maintaining all previous functionalities, including carrying out local structural alignments of sequences with low similarity. Furthermore, the improvements allow for comparing longer RNAs and increasing the sequence length. For example, lengths in the range 2000-6000 nucleotides improve execution up to a factor of five.
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