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. 2016 Apr 15;32(8):1238-40.
doi: 10.1093/bioinformatics/btv748. Epub 2015 Dec 24.

Foldalign 2.5: Multithreaded Implementation for Pairwise Structural RNA Alignment

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Free PMC article

Foldalign 2.5: Multithreaded Implementation for Pairwise Structural RNA Alignment

Daniel Sundfeld et al. Bioinformatics. .
Free PMC article

Abstract

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.

Availability and implementation: The Foldalign software and the web server are available at http://rth.dk/resources/foldalign

Contact: gorodkin@rth.dk

Supplementary information: Supplementary data are available at Bioinformatics online.

Figures

Fig. 1.
Fig. 1.
(a) Parallel design example of two sequences. Every cell corresponds to a bidimensional matrix. Red and blue are cells processed by threads t1 and t2, respectively. Dark red/blue are cells that have already been processed, light red/blue are cells being processed and white or grey are cells to be processed next. The dashed area represents cells that are being read and written by one thread. (b) The Foldalign execution time and memory consumption according to the number of threads. This set contains 5 random sequences with length 6000, GC-content from 40% to 50%, δ= 25 and λ = 1000. The linear speed up is the ideal speedup, when n threads are used and Foldalign is executed n times faster. With 8 threads, the elapsed time is reduced from 4:44 h to 57.1 min (4.98× faster), while consuming 1.99× more memory

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References

    1. Dowell R.D., Eddy S.R. (2006) Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics, 7, 400. - PMC - PubMed
    1. Fu Y. et al. (2014) Dynalign II: common secondary structure prediction for RNA homologs with domain insertions. Nucleic Acids Res., 42, 13939–13948. - PMC - PubMed
    1. Gorodkin J. et al. (2010) De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol., 28, 9–19. - PMC - PubMed
    1. Havgaard J.H. et al. (2007) Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput. Biol., 3, 1896–1908. - PMC - PubMed
    1. Knudsen B., Hein J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res., 31, 3423–3428. - PMC - PubMed
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