Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment

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 - 2016/4/15

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 -