HTS-IBIS - Motif finding from high-throughput SELEX

HTS-IBIS (short for Inferring Binding Sites from HT-SELEX) is a software for inferring binding site motifs from high-throughput SELEX (HT-SELEX). HTS-IBIS takes as input a list of sequence files (in fastq format), correspdonging to each iteration in the experiment and outputs the binding site of the TF as a potision weight matrix. Further details on the functionality of HTS-IBIS are available in the paper listed below.

HTS-IBIS was developed by Yaron Orenstein in Ron Shamir's Computational Genomics group at Tel Aviv University.

Get the software

Java executable distribution

This distribution is our officially supported executable for HTS-IBIS. This binary is completely self-contained and should work out of the box without any issues. The package includes a small test dataset.

The software is freely available under the GNU Lesser General Public License, version 3, or any later version at your choice.

HTS-IBIS is a research tool, still in the development stage. Hence, it is not presented as error-free, accurate, complete, useful, suitable for any specific application or free from any infringement of any rights. The Software is licensed AS IS, entirely at the user's own risk.

How to use it

java -jar HTS-IBIS.jar <output_file> <List of ordered HT-SELEX file from first cycle to last>

HT-SELEX files can be downloaded from ENA, accession numbers ERP001824 and ERP001826.

Example run:

java -jar HTS-IBIS.jar LMX1A.pwm ZeroCycle_TCTGGT20NGGG_0_0.fastq LMX1A_TCTGGT20NGGG_Z_1.fastq LMX1A_TCTGGT20NGGG_Z_2.fastq LMX1A_TCTGGT20NGGG_Z_3.fastq LMX1A_TCTGGT20NGGG_Z_4.fastq

Interpreting the output

On the provided test dataset HTS-IBIS's output should look like this: 
A:	0.183147132396698	0.22810086607933044	0.11032721400260925	0.8135622143745422	0.9158732891082764	. . .	
C:	0.2849732041358948	0.14351284503936768	0.32613304257392883	0.028032639995217323	0.017520010471343994	. . .
G:	0.26065367460250854	0.10847616195678711	0.21236343681812286	0.11921338737010956	0.04402954876422882	. . .
T:	0.2712264955043793	0.5199114084243774	0.35117655992507935	0.03919265791773796	0.022574998438358307	. . .
Each line is of the form nucleotide: [tab] probability_pos_1 [tab] probability_pos_2 [tab] . . .

nucleotide
The line contains probabilities of this nucleotide in all positions.

probability_pos_i
The probability of the nucleotide in position i.

Citing HTS-IBIS

HTS-IBIS can be cited as follows:
HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data
Yaron Orenstein, Ron Shamir.
bioRxiv

Get in touch

In case of any questions or suggestions please feel free to contact Yaron Orenstein.