Shiny App related to G4Hunter published in Bedrat et al. NAR 2016.
Supplementary Data can be downloaded from NCBI or Github.
The EF184640.1.fa file corresponds to the human mitochondrial genome used in the publication.
The hTERC.fa file corresponds to the human telomerase RNA component in RNA alphabet.
The top part of this page allows you to compute the G4Hunter score of a single sequence. This main App (G4Hunter Seeker) identifies DNA or RNA regions in a longer sequence for which the G4Hunter score is above the chosen threshold in windows of the selected size. Please cite "Bedrat A, Lacroix L, & Mergny JL (2016) Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res 44(4):1746-1759.", when reporting results obtained with this App.
- Biostrings
- GenomicRanges
- shiny
1- download the project from github.
2- set the directory where you extract the project as your working directory in R by using the command setwd('PATH_TO_THE_PROJECT').
3- install the required packages by running the install-packages.r script.
4- in the R-console, type runApp().
5- a browser page should open with the app.
6- for the next time you want to run the app, you can just go your R-console and type shiny::runApp('PATH_TO_THE_PROJECT'). Thus if you have installed this app in a directory named work under your home directory, you should type shiny::runApp('~/work/G4HunterSeeker/').
Just type your sequence in the box and you get the G4Hunter score below.
Spaces are automaticaly removed, lower or upper cases are accepted.
Characters orther than G or C are kept and counted as A,T or U.
You have to choose how you enter your sequence either manually (Manual entry) or using a DNA fasta file (Fasta File entry).
You have to choose if your sequence is in the DNA or RNA alphabet.
Please note that mRNA fasta sequences downloaded might use the DNA alphabet.
The Threshold and Window size determine the parameters for the sequence search as described in the publication.
The higher the threshold, the more stringent the search: fewer G4 motifs wil be found, but these will be the most stable/likely ones.
You can change the Target name as you wish, but please note that this name will also end up in the file name of your output file and in the first column of the output table.
Letters in the sequence have to belong to the DNA alphabet (A,C,T,G,M,R,W,S,Y,K,V,H,D,B,N) if DNA alphabet is selected or to the RNA alphabet (A,C,U,G,M,R,W,S,Y,K,V,H,D,B,N) if RNA alphabet is selected.
Gaps (- or .), numbers and hard masking (+) are not accepted.
The file to download has to be a single DNA or RNA fasta file that does not exceed the size limit imposed by Shiny (default is 5Mb, see below how to change it).
The first line of the fasta file (after the > sign) imposes the sequence name (seqname) in the output. This can be changed by checking the Alternate Seqname option and entering the chosen sequence name in the New Seqname option.
The Report sequences option adds the nucleotide sequences in the output.
The Report G_sequences option changes sequences with a negative score (C-rich sequences) into their reverse complement. Thus the output reports only G-rich sequences.
The hits report the number of sequences retrieved that match the settings.
The Length of the Input Sequence corresponds to the length of the DNA sequence you enter with your Fasta file or manually.
The output table contains the sequence name (seqnames), the start, end and width of the refined sequences that meet the search criteria.
The strand is + if the proposed G4 forming sequence is in the Input Sequence and this is set to - if the G4 forming sequence in on the reverse complementary strand.
The score is the G4Hunter score of the refined sequence and max_score is the highest score in absolute value in a window of the chosen window size for the sequence.
Threshold and window are respectively the Threshold and Window size used for the search.
The sequence corresponds to the refined sequence in the Input sequence. This field is sensitive to the Report G-sequences option. This field is not present if the Report sequences option is not selected.
Please note that the procedure extracts sequences that have a G4Hunter score above the threshold (in absolute value) in a window, fuses the overlapping sequences and then refines theses sequences by removing bases at the extremities that are not G for sequences with a positive score (or C the negative ones). It also looks at the first neigboring base and adds it to the sequence if it is a G for sequences with a positive score (C for sequences with a negative score).
Please see the publication and Figure S1B for more details
The output can be exported to a text file that can be directly opened with Microsoft Excel.
As this is a simple Shiny app, there is a limit to the size you can upload (5Mb).
If necessary (but might not be good for the host), the size limit can be increased to XX Mb by adding the following code at the top of the server.R file (adapted from stackoverflow).
options(shiny.maxRequestSize=XX*1024^2)
This project is independent of the G4-Hunter python repository even if both project are related to the same publication.