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SAVoR

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/0000013a-b772-5fba-d69a-d90d80000000

Resource Type

  1. Algorithmic software suite

Properties

  1. Uses algorithmic software component
    RNAfold/RNAplot
  2. Uses algorithmic software component
    SAMTools
  3. Uses algorithmic software component
    BLAST
  4. Resource Description
    "SAVoR is an easy-to-use web application that allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures. SAVoR is designed to help researchers visualize sequencing data in the context of RNA secondary structures. You will find SAVoR useful if: • you want to see the distribution of smRNA-seq reads along a microRNA precursor • you want to see how a set of SNPs might impact RNA structure • you have data from control vs. treatment sequencing experiments and would like to see regions of enrichment along an RNA structure SAVoR has the following features: • Directly retrieve read alignments from web-accessible BAM files • Compute four per-nucleotide scores from read alignments:    - Read abundance    - Endpoint frequency    - Log-ratio of abundance from two RNA-seq experiments    - Frequency of sequence variants (read mismatches) • Accept custom genomic annotations in the UCSC BED file format • Predict RNA secondary structure using multiple methods, or use existing Rfam consensus structures"
  5. Additional Name
    Sequencing Annotation and Visualization of RNA structures
  6. Used by
    Wang Laboratory
  7. Operating System
    Web based
  8. Data Input
    RNA transcript sequence
  9. Data Input
    RNA sequence read alignment
  10. Data Input
    Annotation options
  11. Data Output
    RNA structure model
  12. Data Output
    Coverage annotation values
  13. Software purpose
    Molecular modeling objective
  14. Software purpose
    Data annotation objective
  15. Related Publication or Documentation
    SAVoR: a server for sequencing annotation and visualization of RNA structures
  16. Website(s)
    http://tesla.pcbi.upenn.edu/savor/
  17. Related Technique
    RNA sequencing
 
RDFRDF
 
Provenance Metadata About This Resource Record
  1. workflow state
    Published
  2. contributor
    fcoldren
  3. created
    2012-10-31T11:41:26.878-04:00
  4. creator
    fcoldren
  5. modified
    2013-12-03T15:19:08.704-05:00

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