Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

Daniel Sundfeld; Jakob Hull Havgaard; Alba C. M. A. de Melo; Jan Gorodkin

doi:10.1093/bioinformatics/btv748

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

Daniel Sundfeld, Jakob Hull Havgaard, Alba C. M. A. de Melo, Jan Gorodkin

13 Citations (Scopus)

90 Downloads (Pure)

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.

Original language	English
Journal	Bioinformatics
Volume	32
Issue number	8
Pages (from-to)	1238-1240
Number of pages	3
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btv748
Publication status	Published - 15 Apr 2016

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title = "Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment",

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.",

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AU - Sundfeld, Daniel

AU - Havgaard, Jakob Hull

AU - de Melo, Alba C. M. A.

AU - Gorodkin, Jan

PY - 2016/4/15

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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.

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Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

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