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RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
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Related Experiment Video

Updated: Jun 17, 2026

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Published on: March 25, 2014

High Performance Integration Pipeline for Viral and Epitope Sequences.

Tommaso Alfonsi¹, Pietro Pinoli¹, Arif Canakoglu^1,2

¹Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio 34/5, 20133 Milano, Italy.

Biotech (Basel (Switzerland))

|July 13, 2022

Summary

A new automated pipeline integrates global viral sequences (SARS-CoV-2, MERS, Ebola) from multiple databases, enabling better research and tools like ViruSurf. This enhances the study of viral infections and provides access to millions of sequences.

Keywords:

COVID-19 SARS-CoV-2 bioinformatics data integration metadata management sequence analysis viral datasets

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Area of Science:

Bioinformatics
Virology
Data Science

Background:

The rapid spread of COVID-19 led to daily sharing of numerous viral sequences.
Lack of standardized data across deposition databases hindered practical, homogeneous exploration of global viral sequences.
Existing data repositories lacked comprehensive integration and accessibility for researchers.

Purpose of the Study:

To develop an automated data pipeline for collecting, transforming, and integrating viral sequences from major global databases.
To create efficient and scalable resources for exploring and analyzing viral sequence data.
To support the development of analytical and visualization tools for understanding viral infections.

Main Methods:

Developed an automated pipeline to collect and integrate viral sequences from NCBI, COG-UK, GISAID, and NMDC.
Refined the pipeline for increased efficiency, scalability, and generality, incorporating epitope data from IEDB.
Created data exploration interfaces (VirusViz, EpiSurf) and an integrated database (ViruSurf).

Main Results:

Established ViruSurf, one of the largest integrated viral sequence databases.
The pipeline currently integrates approximately 9.1 million SARS-CoV-2 sequences (March 2022).
Enabled the creation of fundamental research resources and visualization tools like VirusViz and EpiSurf.

Conclusions:

The refined automated pipeline provides a scalable and efficient solution for integrating diverse viral sequence data.
This work significantly enhances the ability of researchers to study viral mechanisms and evolution.
The developed resources and tools are crucial for advancing research in virology and infectious diseases.