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NoFold

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/0000014b-c152-8809-d034-1ff680000000

Resource Type

  1. Algorithmic software suite

Properties

  1. Resource Description
    "NoFold is an approach for characterizing and clustering RNA secondary structures without computational folding or alignment. It works by mapping each RNA sequence of interest to a structural feature space, where each coordinate within the space corresponds to the probabilistic similarity of the sequence to an empirically defined structure model (e.g. Rfam family covariance models). NoFold provides scripts for mapping sequences to this structure space, extracting any robust clusters that are formed, and annotating those clusters with structural and functional information."
  2. Used by
    Kim Laboratory: Computational Evolutionary Biology
  3. Operating System
    UNIX
  4. Data Input
    RNA sequences
  5. Data Input
    Rfam covariance models
  6. Data Output
    detailed annotation of each final cluster
  7. Data Output
    summary stats for each final cluster
  8. Data Output
    cluster-CMs
  9. Data Output
    predicted structures of each threshold-passing cluster
  10. Software purpose
    RNA family classification objective
  11. Related Publication or Documentation
    NoFold: RNA structure clustering without folding or alignment
  12. Website(s)
    http://kim.bio.upenn.edu/software/nofold.shtml
  13. Developed by
    Kim Laboratory: Computational Evolutionary Biology
  14. Software license
    Academic software license
  15. Coded in
    Python
 
RDFRDF
 
Provenance Metadata About This Resource Record
  1. workflow state
    Published
  2. contributor
    fcoldren
  3. created
    2015-02-25T10:19:52.153-05:00
  4. creator
    fcoldren
  5. modified
    2015-02-25T11:46:27.033-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016