LIRBase

A total of 427 eukaryote genomes were collected and the long inverted repeats (LIR, longer than 800 nt) in these genomes were systematically identified. The following functionalities are implemented in LIRBase.

1. Browse LIRs identified in 427 eukaryotic genomes for the sequences, structures of LIRs, and the overlaps between LIRs and genes.
2. Search LIRBase for LIRs in a specific genome by genomic locations.
3. Search LIRBase for LIRs in a specific genome by the identifiers of LIRs.
4. Search LIRBase by sequence similarity using BLAST.
5. Detect and annotate LIRs in user-uploaded DNA sequences.
6. Align small RNA sequencing data to LIRs of a specific genome to detect the origination of small RNAs from LIRs and quantify the expression level of small RNAs and LIRs.
7. Perform differential expression analysis of LIRs or small RNAs between different biological samples/tissues.
8. Identify protein-coding genes targeted by the small RNAs derived from a LIR through detecting the complementary matches between small RNAs and the cDNA sequence of protein-coding genes.
9. Predict and visualize the secondary structure of potential hpRNA encoded by a LIR using RNAfold.

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Use LIRBase online

LIRBase is deployed at venyao.xyz/lirbase/ for online use.

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Deploy LIRBase on local or web Linux server

Step 1: Install R

Please check CRAN (cran.r-project.org) for the installation of R.

Step 2: Install the R Shiny package and other packages required by LIRBase

Start an R session and run these lines in R:

# try an http CRAN mirror if https CRAN mirror doesn't work  
install.packages("data.table")
install.packages("DT")
install.packages("ggplot2")
install.packages("grid")
install.packages("gridExtra")
install.packages("htmlwidgets")
install.packages("pheatmap")
install.packages("RColorBrewer")
install.packages("shiny")
install.packages("shinyBS")
install.packages("shinycssloaders")
install.packages("shinydashboard")
install.packages("shinydisconnect")
install.packages("shinyjqui")
install.packages("shinyWidgets")
install.packages("stringr")
install.packages("tidyr")
install.packages("dplyr")
install.packages("XML")

install.packages("BiocManager")
BiocManager::install("apeglm")
BiocManager::install("Biostrings")
BiocManager::install("DESeq2")
BiocManager::install("GenomicRanges")

# install shinysky
install.packages("devtools")
devtools::install_github("venyao/ShinySky", force=TRUE)

For more information, please check the following pages:
cran.r-project.org/web/packages/shiny/index.html
github.com/rstudio/shiny
shiny.rstudio.com

Step 3: Install Shiny-Server

Please check the following pages for the installation of shiny-server.
rstudio.com/products/shiny/download-server/
github.com/rstudio/shiny-server/wiki/Building-Shiny-Server-from-Source

Step 4: Install BLAST+

Download and install BLAST+ on your system PATH. Check opensource.com/article/17/6/set-path-linux for the setting of system PATH in Linux.
Please check blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download for the download and installation of BLAST+.

Step 5: Install Bowtie

Download and install Bowtie on your system PATH. Check opensource.com/article/17/6/set-path-linux for the setting of system PATH in Linux.
Please check bowtie-bio.sourceforge.net/index.shtml and github.com/BenLangmead/bowtie for the download and installation of Bowtie.

Step 6: Upload source files of LIRBase

Put the directory containing the code and data of LIRBase to /srv/shiny-server.
The BLASTN database files downloaded from the Data menu of LIRBase should be placed in the LIRBase_blastdb directory under the www directory of LIRBase.
The downloaded Bowtie index files downloaded from the Data menu of LIRBase should be placed in the LIRBase_bowtiedb directory under the www directory of LIRBase.
The downloaded Inverted_repeat_structure files downloaded from the Data menu of LIRBase should be placed in the Table directory under the www directory of LIRBase.
The downloaded Inverted_repeat_sequence files downloaded from the Data menu of LIRBase should be placed in the Fasta directory under the www directory of LIRBase.
The downloaded IRF_stem_alignment files downloaded from the Data menu of LIRBase should be placed in the HTML directory under the www directory of LIRBase.

Step 7: Configure shiny server (/etc/shiny-server/shiny-server.conf)

# Define the user to spawn R Shiny processes
run_as shiny;

# Define a top-level server which will listen on a port
server {  
  # Use port 3838  
  listen 3838;  
  # Define the location available at the base URL  
  location /lirbase {  
    # Directory containing the code and data of LIRBase  
    app_dir /srv/shiny-server/LIRBase;  
    # Directory to store the log files  
    log_dir /var/log/shiny-server;  
  }  
}  

Step 8: Change the owner of the LIRBase directory

$ chown -R shiny /srv/shiny-server/LIRBase  

Step 9: Start Shiny-Server

$ start shiny-server  

Now, the LIRBase app is available at http://IPAddressOfTheServer:3838/LIRBase/ (Remeber to replace IPAddressOfTheServer as the actual IP address of your Linux server).