Bioinformatics

About

Volcani Bioinformatics Unit:

In 2025, the Bioinformatics Unit continued to provide professional service alongside industry collaborations. Service areas included: transcriptome analysis in plant pathogens and plants, locating sources of variation in plant genomes, evolutionary analysis (phylogeny) of genes from plants and plant pathogens, genomic comparisons, and metagenomic analysis of soil bacteria.

New fields introduced this year:

Research data management and digitization – For over a decade, the Unit has managed genomic data from a variety of crops. This year, a pipeline was implemented allowing for the integration of data into a genomic portal. The first portal was established this year for the Cucurbit group, and two additional portals are currently being built. We hope to expand the initiative and achieve full digitization of genomic information within the administration. The project was carried out in collaboration with TDM (the Computing Unit).

Use of advanced AI tools to predict the functional effect of genetic variation:
AlphaFold (by Google DeepMind) is AI-based software for predicting the 3D structure of proteins. The revolutionary ability of AlphaFold 2 (December 2020) to predict the 3D structure of a protein from a primary sequence with high accuracy, within minutes, opens new horizons in the fields of precision medicine, drug development, understanding diseases, protein engineering, and also in agriculture and industrial biotechnology.

This year, as part of a program to implement software from the field of Artificial Intelligence, a pipeline was developed in the Unit that enables the use of AlphaFold to predict the effect of genetic variation on the phenotype.

New order

Click here to place a new order

Research and analysis services

The unit provides a wide range of services in accordance with the research needs. The main analysis currently performed is detailed below.  We are constantly making an effort to update the range of services and tools.

Transcriptome Sequences assembly: De-novo transcriptome assembly of non-model species based on next generation sequencing from Illumina technology.

Annotation of Transcriptome : Transcripts annotation based on sequences similarity to available database sequences (i.e.: NCBI databases and UniProt)

RNA-Seq analysis : Differential expression analysis and cluster analysis. Functional analysis of the differentially expressed genes, including GO term, and pathway enrichment analysis.

Genotype By Sequencing (GBS) data analysis: Genome-wide SNP discovery by combining the power of multiplexed NGS. Tassel-GBS pipeline is used for the analysis.

Variant Calling: Variant calling or SNP discovery based on NGS data. Quality control and filter steps are performed to provide reliable data.

Phylogenetic analysis:  Explore evolutionary relationships among organisms or genes based on genetic data.

Metagenomic analysis: Identification of microbial and fungi communities from sequences of 16S/18S rRNA and from metagenomic sequencing data.

Team

Volcani Bioinformatics Unit is located in the Volcani center, Institute of Plant Sciences, Crop Science build:

Adi Faigenboim, Ph.D.: Room 1037, adif@volcani.agri.gov.il

Noa Sela, Ph.D.: Room 1034, noa@volcani.agri.gov.il

Arye Harel, Ph.D.: Room 1034, aryeharel@volcani.agri.gov.il

Gon Carmi, Ph.D.: Newe Ya’ar Research Center, gonc@volcani.agri.gov.il

Volcani Bioinformatics Unit:

In 2025, the Bioinformatics Unit continued to provide professional service alongside industry collaborations. Service areas included: transcriptome analysis in plant pathogens and plants, locating sources of variation in plant genomes, evolutionary analysis (phylogeny) of genes from plants and plant pathogens, genomic comparisons, and metagenomic analysis of soil bacteria.

New fields introduced this year:

Research data management and digitization – For over a decade, the Unit has managed genomic data from a variety of crops. This year, a pipeline was implemented allowing for the integration of data into a genomic portal. The first portal was established this year for the Cucurbit group, and two additional portals are currently being built. We hope to expand the initiative and achieve full digitization of genomic information within the administration. The project was carried out in collaboration with TDM (the Computing Unit).

Use of advanced AI tools to predict the functional effect of genetic variation:
AlphaFold (by Google DeepMind) is AI-based software for predicting the 3D structure of proteins. The revolutionary ability of AlphaFold 2 (December 2020) to predict the 3D structure of a protein from a primary sequence with high accuracy, within minutes, opens new horizons in the fields of precision medicine, drug development, understanding diseases, protein engineering, and also in agriculture and industrial biotechnology.

This year, as part of a program to implement software from the field of Artificial Intelligence, a pipeline was developed in the Unit that enables the use of AlphaFold to predict the effect of genetic variation on the phenotype.