HELIANO: A fast and accurate tool for detection of Helitron-like elements.

Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging to identify. Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements. Please check wiki for detailed usage.

Update Note
Dependencies
Installation
Usage
References
FAQ
Release history
To contact us

Update Note:

Since version 1.1.0, HELIANO will use the term HLE1 to refer to the canonical Helitron (called Helitron in v1.0.2) and the term HLE2 to refer to the non-canonical Helitrons (called HLE2 in v1.0.2). See figure below:

From version 1.1.0, users are allowed to input a pair file as a complementary for LTS-RTS pair information. This will help a lot in searching for HLEs in close species. For more information, see here.

Dependencies

- python = 3.9.0
- r-base = 4.1
- biopython
- pybedtools = 0.9.0 =py39hd65a603_2
- r-bedtoolsr
- r-seqinr = 4.2_16 = r41h06615bd_0
- bedtools = 2.30.0
- dialign2 = 2.2.1
- mafft
- cd-hit = 4.8.1
- blast = 2.2.31
- emboss = 6.6.0
- hmmer = 3.3.2
- genometools-genometools = 1.6.2 = py39h58cc16e_6
- rnabob = 2.2.1

Installation

mamba (Recommendation)

If mamba is not installed on your system, you can install it with the following commands easily.

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh -b

Then you can install HELIANO with mamba.

#create the HELIANO environment
mamba create -n HELIANO
#activate the HELIANO environment
mamba activate HELIANO
# install 
mamba install zhenlisme::HELIANO -c conda-forge -c bioconda
mamba deactivate

conda

#create the HELIANO environment
conda create -n HELIANO
#activate the HELIANO environment
conda activate HELIANO
# installation 
conda install zhenlisme::HELIANO -c conda-forge -c bioconda
conda deactivate

manual installation

Before installation, you need to be sure that all dependencies have been installed on your computer and that their path are defined in your environmental variables. All dependencies could be installed via conda/mamba.

download the latest HELIANO package.
git clone https://github.com/Zhenlisme/HELIANO.git
switch to the source code dorectory that you cloned at the last step.
cd HELIANO/
run configure file.
bash configure.sh
You can find HELIANO in the bin directory.

Usage

Activate the HELIANO conda environment (for conda/mamba installation)

conda activate HELIANO

Perform a test run of HELIANO

Here we will use the chromosome 18 of Fusarium oxysporum strain Fo5176 as an example, where you can find it in file test.fa .

Perform the following code: heliano -g test.fa -is1 0 -is2 0 -o test_opt -w 15000

HELIANO outputs

You will find two main result files when HELIANO program runs successfully.

RC.representative.bed: the predicted HLE1/HLE2 coordinates in bed format (available in the file test.opt.tbl in this repository).
RC.representative.fa: the predicted HLE1/HLE2 sequences in fasta format.
pairlist.tbl: The file for LTS-RTS pair information. Other files or directories are intermediate outputs.
TIR_count.tbl: Table for counts of terminal inverted repeats of each HLE subfamily.
Boundary.tbl: Table for the conservation of flanking regions of each HLE subfamily.
HLE1/ or HLE2/: Directory for intermediate files when detecting HLE1/HLE2.

Explanation for RC.representative.bed

There are 11 columns in RC.representative.bed file:
|chrm-id|start|end|subfamily|occurence|strand|pvalue|TS_blastn_identity|variant|type|name| | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | |CP128282.1|53617|59046|HLE2_left_18-HLE2_right_18|7|-|6.3390e-07|60|HLE2|auto|insertion_HLE2_auto_1| |CP128282.1|83425|88824|HLE2_left_18-HLE2_right_18|7|-|6.3390e-07|60|HLE2|auto|insertion_HLE2_auto_2| |CP128282.1|94525|99924|HLE2_left_18-HLE2_right_18|7|+|6.3390e-07|60|HLE2|auto|insertion_HLE2_auto_3| |CP128282.1|306838|312276|HLE2_left_18-HLE2_right_18|7|+|6.3390e-07|60|HLE2|auto|insertion_HLE2_auto_4|

Detailed explaination for each column.

Notice: The insertions that encode Rep/helicase are considered putative autonomous HLEs. |Columns|Explaination| | ---- | ---- | |chrm-id|chromosome id| |start|start site of HLE| |stop|stop site of HLE| |subfamily|heliano classification| |occurence|how often this subfamily occurred in genome| |strand|the insertion is on which strand| |pvalue|pvalue of fisher's exact test, indicating the significance of the prediction. The lower, the more significant.| |TS_blastn_identity|the average identity of RTS and LTS to their representative counterparts| |variant|the insertion is HLE1 or HLE2| |type|the mobility of HLE, either autonomous (auto) or nonautonomous (nonauto)| |name|unique identifier for each insertion|

Generation for consensus sequences

The HELIANO package also provides a program (heliano_cons) for generating consensus sequences of HLE.
Check the usage of heliano_cons:
heliano_cons -h

usage: heliano_cons [-h] -g GENOME -r REPSENBED -o OPDIR [-n PROCESS] [-v]

Making consensus for Helitron-like sequences. Please visit https://github.com/Zhenlisme/heliano/ for more information. Email us: zhen.li3@universite-paris-saclay.fr

optional arguments:
  -h, --help            show this help message and exit
  -g GENOME, --genome GENOME
                        The genome file in fasta format.
  -r REPSENBED, --repsenbed REPSENBED
                        The representative bed file (RC.representative.bed).
  -o OPDIR, --opdir OPDIR
                        The output directory.
  -n PROCESS, --process PROCESS
                        Maximum of threads to be used.
  -v, --version         show program's version number and exit

Dis-denovo prediction

Since version 1.1.0, HELIANO enables prediction of HLEs with the help of pre-identified LTS-RTS pair file. The pairlist.tbl can be either obtained from the main directory of your previous run or user-defined.

You can skip the denovo prediction of the LTS-RTS pair process (will save a lot of time),

heliano -g test.fa -is1 0 -is2 0 -o test_opt -w 15000 -ts pairlist.tbl --dis_denovo

Or not skip the de novo prediction of the LTS-RTS process

heliano -g test.fa -is1 0 -is2 0 -o test_opt -w 15000 -ts pairlist.tbl

References

If you find HELIANO useful to you, please cite:

Li Z , Gilbert C , Peng H , Pollet N. "Discovery of numerous novel Helitron-like elements in eukaryote genomes using HELIANO." Nucleic Acids Research, 2024. doi: doi.org/10.1093/nar/gkae679.

Li Z , Pollet N. "HELIANO: a Helitron-like element annotator." Zenodo (2024). doi: 10.5281/zenodo.10625239

Frequently asked questions

1. How to get fragmented copies of HLEs?

HELIANO is designed to predict complete insertions of Helitron-like elements (HLE), with the limitation that fragmented insertions will not be reported. To identify fragmented insertions, we recommend running RepeatMasker or BLASTN using HELIANO predictions as the query. Before you run RepeatMasker or BLASTN, we suggest masking the HLE query with a trusted non-HLE TE database because other non-HLE TEs might insert into long HLEs, which would inflate sequence length and result in misannotation.

2. How to choose parameters properly?

For a precise and quick search, you can use the stringent parameter '-is1 1 -is2 1 -p 1e-5 -s 30 -pt 1 -sim_tir 100' that considers the preferred insertion sites of HLE. For big or complex genomes (e.g., the maize genome), I just recommend you use the stringent parameter set. But not all HLEs obey their regular preferred insertion sites. If you want to explore more in your interested genome, you can use the loose parameter set, e.g., '-is1 0 -is2 0 -sim_tir 90', and you will have more predictions and a longer execution time. Note that the parameters '-is2' and '-sim_tir' are only for HLE2s, and '-is1' and '-pt' are only for Helitrons.

Replace the term Helitron with HLE1 and Helentron with HLE2.
Enable to prediction of HLEs based on a pre-identified LTS-RTS pair file. (see -ts and --dis_denovo para

Heliano

Install / Use

README