InversFinder: A Bioinformatics Tool for Finding Inversions and RNA Segmentation

Software Version: InversFinder 2.0 March 2015
Document Author: RNAVLab, Bioinformatics Program, UTEP
Email: rnavlab@utep.edu

Table of Contents for Release Notes: Updated 3/2/2015
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1. Root Directory (\InversFinder20) and Output Subdirectory (\InversFinder20\inverslist)
2. Use of FASTA and Knowlegde of Sequence Inversions
3. R Environment (GUI) Required for Running Segmenta 2.0
4. Find Inversions, Prepare Inversion List, and Run Segmentation
5. Update in Version 2.0.150302 for Including Smaller Overlapping Inversions as Default
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1. Root Directory (\InversFinder20) and Output Subdirectory (\InversFinder20\inverslist)
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After unzipping the InversFinder20.zip file, the root directory (\InversFinder20) for the 
InversFinder20.jar executive file and output subdirectory (\InversFinder20\inverslist) 
for chunk files and PDF plots will be created automatically.

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2. Use of FASTA Files and Knowledge of Sequence Inversions
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Sequence file must be prepared in FASTA format and placed in the root directory for 
loading. Type the filename in the first input field or click "Browse" to select the 
.fasta file, and click the radio buttons for optional choices in finding the inversions.
In addition, you may select your own starting and ending values of minimum stem lengths, 
maximum gaps, and number of mismatches allowed for InversFinder to run iteratively 
within the ranges. Default entries will show up after clicking the "Find Inversions" 
button and you may edit those values. 


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3. R Environment (GUI) Required for Running Segmenta 2.0
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In addition to the Java environment, InversFinder 2.0 requires R to be installed on your 
computer running either 32-bit and 64-bit Windows 7, and Version 2.14.2 is recommended. 
For other versions, you may click the "Browse" button for finding "Path for R" in the 
lower left-hand corner of InversFinder 2.0. 

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4. Find Inversions, Prepare Inversion List, and Run Segmentation
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After finding the inversions, you may type in your own file name for the generated output 
file or you may just use the default one. Before running RNA segmentation, you have to 
click the "Prepare Inversion List" to generate files in the inverslist directory to be 
used by Segmenta 2.0. Then, you may enter the value of Maximum Chuck Size (C) or use the 
default of 100, and click "Run Segmentation" for the GUI version of R to load, where you 
select "Source R Code..." under the File menu. Highlight "Segmenta20.r" and click the 
file to run the program. Output text, FASTA, and PDF Rplot files will be place in 
inverslist subdirectory. The FASTA files for chucks after segmentation can be loaded
directly to RNASSA 2.0 for prediction.

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5. Update in Version 2.0.150302 for Including Smaller Overlapping Inversions as Default
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In previous versions, the default was excluding overlaps and to include them by clicking
the radio button "Report overlaps." In this release, the results will include overlaps by
default and user has to click the radio "Exclude inversions inside longer ones" to
exclude this type of inversions.

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Please email us at rnavlab@utep.edu immediately if you encounter problems or have 
comments. The latest version is InversFinder 2.0.150302.