GIREMI 0.2.1 – Genome-independent Identification of RNA Editing by Mutual Information

GIREMI 0.2.1

:: DESCRIPTION

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.

::DEVELOPER

XIAO LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R
  • C++ Compiler

:: DOWNLOAD

 GIREMI

:: MORE INFORMATION

Citation:

Nat Methods. 2015 Mar 2. doi: 10.1038/nmeth.3314.
Genome sequence-independent identification of RNA editing sites.
Zhang Q, Xiao X

RCARE – RNA-Seq Comparison and Annotation of RNA Editing

RCARE

:: DESCRIPTION

RCARE searches, annotates and visualizes RNA editing sites using previously known thousands of editing sites.

RCARE conversion utilities is a set of python-based utilities which convert FASTQ and BAM(binary format for storing sequence data) into VCF(variant call format) and compare RNA to DNA VCF files which are derived from the same sample.

::DEVELOPER

SNUBI (Snubi’s Not Unics, Biomedical Informatics.)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RCARE conversion utilities

:: MORE INFORMATION

Citation:

BMC Med Genomics. 2015 May 29;8 Suppl 2:S8. doi: 10.1186/1755-8794-8-S2-S8.
RCARE: RNA Sequence Comparison and Annotation for RNA Editing.
Lee S, Joung JG, Park C, Park J, Kim JH.

AIRlINER – Assessment of A-to-I RNA Editing Sites in Non-repetitive Regions

AIRlINER

:: DESCRIPTION

AIRlINER is an algorithmic approach to the assessment of A-to-I  (Adenosine-to-Inosine)  RNA editing sites in non-repetitive regions. It determines the editing probability of an adenosine by analyzing its flanking region of 10 nucleotides. Such pattern is then combined with a similar model calculated from un-edited sequences, resulting in the estimation of an unbiased editing probability.

::DEVELOPER

AIRlINER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Knowledge in the Investigation of A-to-I RNA Editing Signals.
Nigita G, Alaimo S, Ferro A, Giugno R, Pulvirenti A.
Front Bioeng Biotechnol. 2015 Feb 24;3:18. doi: 10.3389/fbioe.2015.00018.

ExpEdit – Webserver to Explore human RNA Editing in RNA-Seq experiments

ExpEdit

:: DESCRIPTION

ExpEdit is a web application for assessing RNA editing in human at known or user-specified sites supported by transcript data obtained by RNA-Seq experiments.

::DEVELOPER

ExpEdit team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 1;27(9):1311-2. doi: 10.1093/bioinformatics/btr117. Epub 2011 Mar 22.
ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.
Picardi E1, D’Antonio M, Carrabino D, Castrignanò T, Pesole G.

REDItools 1.0.4 – RNA editing detection by NGS data

REDItools 1.0.4

:: DESCRIPTION

REDItools are python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.

::DEVELOPER

REDItools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 REDItools

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2015 Mar 9;49:12.12.1-12.12.15. doi: 10.1002/0471250953.bi1212s49.
Using REDItools to Detect RNA Editing Events in NGS Datasets.
Picardi E1, D’Erchia AM, Montalvo A, Pesole G.