Database Commons a catalog of biological databases

Database Commons - FoldAtlas

FoldAtlas

Citations: 1

z-index 1.00

Short name FoldAtlas
Full name
Description a repository for genome-wide RNA structure probing data
URL http://www.foldatlas.com/
Year founded 2016
Last update & version 2016-09-22    v 1.1
Availability Free to all users
University/Institution hosted Norwich Research Park
Address John Innes Centre
City Norwich
Province/State
Country/Region United Kingdom
Contact name Yiliang Ding
Contact email yiliang.ding@jic.ac.uk
Data type(s)
Major organism(s)
Keyword(s)
  • RNA secondary structure
Publication(s)
  • FoldAtlas: a repository for genome-wide RNA structure probing data. [PMID: 27663500]

    Matthew Norris, Chun Kit Kwok, Jitender Cheema, Matthew Hartley, Richard J Morris, Sharon Aviran, Yiliang Ding
    Bioinformatics (Oxford, England) 2017:33(2)
    1 Citations (Google Scholar as of 2017-04-06)

    Abstract: Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work. The FoldAtlas website can be accessed at www.foldatlas.com Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985. yiliang.ding@jic.ac.uk or matthew.norris@jic.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Community reviews

Data
quality & quantity
Content organization & presentation
System accessibility & reliability
Reviewed by

Word cloud (embeddable)

Database Commons - Word Cloud

Accessibility

Rate of accessibility:
HTTP status codeDate requested
200 OK2017-10-17
200 OK2017-10-13
200 OK2017-10-10
200 OK2017-10-06
200 OK2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
200 OK2017-05-30
200 OK2017-05-26
200 OK2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
200 OK2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07

Tags

RNA Structure
Arabidopsis thaliana
RNA secondary structure

Record metadata

  • Created on: 2017-04-06
  • Curated by:
    • Shixiang Sun [2017-04-06]
Stats