Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

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Standard

Foldalign 2.5 : multithreaded implementation for pairwise structural RNA alignment. / Sundfeld, Daniel; Havgaard, Jakob Hull; de Melo, Alba C. M. A.; Gorodkin, Jan.

I: Bioinformatics, Bind 32, Nr. 8, 2016, s. 1238-1240.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Sundfeld, D, Havgaard, JH, de Melo, ACMA & Gorodkin, J 2016, 'Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment', Bioinformatics, bind 32, nr. 8, s. 1238-1240. https://doi.org/10.1093/bioinformatics/btv748

APA

Sundfeld, D., Havgaard, J. H., de Melo, A. C. M. A., & Gorodkin, J. (2016). Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment. Bioinformatics, 32(8), 1238-1240. https://doi.org/10.1093/bioinformatics/btv748

Vancouver

Sundfeld D, Havgaard JH, de Melo ACMA, Gorodkin J. Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment. Bioinformatics. 2016;32(8):1238-1240. https://doi.org/10.1093/bioinformatics/btv748

Author

Sundfeld, Daniel ; Havgaard, Jakob Hull ; de Melo, Alba C. M. A. ; Gorodkin, Jan. / Foldalign 2.5 : multithreaded implementation for pairwise structural RNA alignment. I: Bioinformatics. 2016 ; Bind 32, Nr. 8. s. 1238-1240.

Bibtex

@article{e1994d7ba628469990ad50c76a165233,
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.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.",
author = "Daniel Sundfeld and Havgaard, {Jakob Hull} and {de Melo}, {Alba C. M. A.} and Jan Gorodkin",
note = "{\textcopyright} The Author 2015. Published by Oxford University Press.",
year = "2016",
doi = "10.1093/bioinformatics/btv748",
language = "English",
volume = "32",
pages = "1238--1240",
journal = "Computer Applications in the Biosciences",
issn = "1471-2105",
publisher = "Oxford University Press",
number = "8",

}

RIS

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