Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2016 Apr 15;32(8):1238-40. doi: 10.1093/bioinformatics/btv748. Epub 2015 Dec 24.

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.

Author information

  • 1Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and Department of Computer Science, University of Brasilia, Brasília, DF, Brazil.
  • 2Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and.
  • 3Department of Computer Science, University of Brasilia, Brasília, DF, Brazil.

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 http://rth.dk/resources/foldalign

CONTACT:

gorodkin@rth.dk

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26704597
PMCID:
PMC4824132
DOI:
10.1093/bioinformatics/btv748
[PubMed - in process]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center