IRscope is a tool for visualizing the genes on the boundaries of the junction sites of the chloroplast genome. The input files can be uploaded using the 'Files upload' tab. After the submission, the program will start searching the Inverted Repeat regions. Note that the species selected will lead to a consensus radius for each junction site for the genes to be plotted. This indicates that if the input files are not representing closely related species, the program may lead to unsatisfactory result. Finally note that the input files can be either manual annotations, GeneBank accession numbers, or related GB files of the chloroplast genomes.
You need to provide information related to at least two species for the analysis to proceed. After you have successfully provided your input files, press the 'Submit' button. This will activate its following box. Be patient till you are communicated through that box on how to proceed for downloading your output. Also note that the computations may take up to five minutes. Please be patient. For running the analysis, one can use either of the following cases.
1. GB FilesIn this method, you can provide the GB files or the accession number of the related species to obtain the IR plot. This function is active under the 'GB File' tab
2. Manual FilesThis method is useful for the times when simple tabular format of the annotations, the genome sequences of the targeted species, and possibly their corresponding inverted repeat regions boundary coordinates are available. This function is active under 'Manual Files' tab.
Further instructions for each case is given specifically under relevant tab.
In this section you can upload either your GeneBank files or provide their corresponding accession numbers if applicable. You can denote if you want to depict the SSC region in the reverse order by ticking the 'SSC', box for a corresponding input file.
For example, you can test the program with these accession numbers:
After submission the section below will turn innactive, meaning that analysis is in process. Be patient until you are prompted to download your plot.
In case your GB files are of low quality or otherwise not available and still you would like to obtain the plot, you can provide your annotations as a simple tabular format (primary
DOGMA
output) beside their genomes in fasta format and proceed to obtain the plot. In case you also have the values for the junction sites coordinates, you can provide them on the 'IR info' section as JLB, JSB, JSA, and JLA respectively. This decreases the processing time dramatically and would be useful in cases where for example the IR regions are not identical.
A minimal example of a annotation input can be like
this
file.
After submission the section below will turn innactive, meaning that analysis is in process. Be patient until you are prompted to download your plot.
A: Check your input file(s), IRscope is based on the gene names specified in them.
A: This is due to the bad annotation implemented in the input file(s). Often this is related to the genes with introns or trans-spliced genes like rps12. Check and fix your input files.
A: IRscope can handle the redundant base pairs but if the sequence is of a very poor quality the program may fail in detecting the inverted regions and hence not produce any output.
A: This is mostly because at least one of your species differs significantly from the rest so that it creates too large radius for finding the genes in the vicinity of the junction site and consequently causes the populated genes in these respective areas. Try reducing the species sampling to a smaller group of more closely related species.
A: Yes, please download the file in the 'About' section, run the whole script in your R session. This will set up a pseudo web interface on your computer which resemles and works exactly like the online version. You can further tune the functions as you wish.
A: Yes, after downloading the file in the 'About' section, alter the 'parallel' arguments of the function 'IRinfo' into 'TRUE'. Then run the whole code on your R console. This will launch an instance with default 4 CPUs. If your machine is equipped with more cores, you can increase the number of CPUs with the 'nCPU' in 'p.d' subfunction inside the 'IRinfo' function.
A: This should be a plain text format (.txt) of the four tab separated columns, as start of the gene, end of the gene, its name, and the direction of it (+ or -). Note that the file needs to be without header.
A: The genome names in the 'GB Files' are read from the 'Organism' line of the file while the first space separated text of the genomes first line in the manual part is a determinant of species name in this section. In the 'Manual Files' section, the names are read from the first line after the '>' of the fasta file uploaded. Please edit them if they do not follow your expectations and rerun.
A: The IRscope is primarily optimized for the angiosperms and it often turns reliable results for other seed plants as well. However, further departure from the Embryophyta will extend this program to its limits. In such cases, you may want to consider use of the manual section with providing the the IR coordinates.
A: The paper describing this web app in detail with the title IRscope: An online program to visualize the junction sites of chloroplast genomes is submitted to Bioinformatics journal. Please, cite the paper when you use the program.
IRscope and its all dependencies are coded in R. The detailed instruction on how to use each subfuction is provided as well. Also the accession numbers that used to test and train the program are listed at the end of the file. Click here to download the file after which, you can run all the codes (apart from accession numbers) into your R Console to obtain this app on your PC. Here are two example outputs of the program: example1 and example2 .
The paper describing this web app in detail with the title IRscope: An online program to visualize the junction sites of chloroplast genomes is submitted to Bioinformatics journal. Please cite that papers in all your correspondence. In case of practical issues please consult the FAQ sections first or email us at ali(dot)amiryousefi@helsinki(dot)fi.