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 Citationer (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.

Originalsprog	Engelsk
Tidsskrift	Bioinformatics
Vol/bind	32
Udgave nummer	8
Sider (fra-til)	1238-1240
Antal sider	3
ISSN	1367-4803
DOI	https://doi.org/10.1093/bioinformatics/btv748
Status	Udgivet - 15 apr. 2016

Adgang til dokumentet

10.1093/bioinformatics/btv748

Foldalign 2.5Forlagets udgivne version, 167 KB
btv748.pdfForlagets udgivne version, 212 KB

Citationsformater

@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.",

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",

month = apr,

day = "15",

doi = "10.1093/bioinformatics/btv748",

language = "English",

volume = "32",

pages = "1238--1240",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "8",

}

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

PY - 2016/4/15

Y1 - 2016/4/15

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.

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.

U2 - 10.1093/bioinformatics/btv748

DO - 10.1093/bioinformatics/btv748

M3 - Journal article

C2 - 26704597

SN - 1367-4803

VL - 32

SP - 1238

EP - 1240

JO - Bioinformatics

JF - Bioinformatics

IS - 8

ER -

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

Abstract

Adgang til dokumentet

Fingeraftryk

Citationsformater