Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
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Foldalign 2.5 : multithreaded implementation for pairwise structural RNA alignment. / Sundfeld, Daniel; Havgaard, Jakob Hull; de Melo, Alba C. M. A.; Gorodkin, Jan.
In: Bioinformatics, Vol. 32, No. 8, 2016, p. 1238-1240.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Foldalign 2.5
T2 - multithreaded implementation for pairwise structural RNA alignment
AU - Sundfeld, Daniel
AU - Havgaard, Jakob Hull
AU - de Melo, Alba C. M. A.
AU - Gorodkin, Jan
N1 - © The Author 2015. Published by Oxford University Press.
PY - 2016
Y1 - 2016
N2 - 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 https://rth.dk/resources/foldalign CONTACT: gorodkin@rth.dkSupplementary information: Supplementary data are available at Bioinformatics online.
AB - 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 https://rth.dk/resources/foldalign CONTACT: gorodkin@rth.dkSupplementary information: Supplementary data are available at Bioinformatics online.
U2 - 10.1093/bioinformatics/btv748
DO - 10.1093/bioinformatics/btv748
M3 - Journal article
C2 - 26704597
VL - 32
SP - 1238
EP - 1240
JO - Computer Applications in the Biosciences
JF - Computer Applications in the Biosciences
SN - 1471-2105
IS - 8
ER -
ID: 160608259