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Updated: Jun 8, 2025

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

TransAnnot-a fast transcriptome annotation pipeline.

Mariia Zelenskaia¹, Yazhini Arangasamy¹, Milot Mirdita²

¹Quantitative and Computational Biology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.

Bioinformatics Advances

|November 4, 2024

Summary

This summary is machine-generated.

TransAnnot is a new, fast, and user-friendly pipeline for transcriptome annotation. It automates homology searches, gene ontology, and domain annotation, significantly improving speed over existing tools.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Transcriptome annotation is crucial for understanding gene function.
Current annotation tools can be slow, complex to install, and difficult to use, hindering research.
There is a need for efficient and accessible transcriptome annotation solutions.

Purpose of the Study:

To develop TransAnnot, a fast, automated, and user-friendly transcriptome annotation pipeline.
To address the limitations of existing state-of-the-art annotation tools.
To provide a streamlined solution for annotating de novo assembled transcriptomes.

Main Methods:

TransAnnot utilizes the MMseqs2 suite for rapid sequence searches.
It integrates annotation against Swiss-Prot, eggNOG, and Pfam databases.
The pipeline accepts various input formats, including sequencing reads and nucleotide/amino acid sequences.
Users can also annotate against custom databases.

Main Results:

TransAnnot provides one-step annotation of homologs, gene ontology terms, orthogroups, and functional domains.
Benchmarking demonstrated TransAnnot to be significantly faster than EnTAP, Trinotate, and eggNOG-mapper.
TransAnnot achieved speed improvements of 333x, 284x, and 18x, respectively.

Conclusions:

TransAnnot offers a substantial speed improvement for transcriptome annotation.
Its ease of installation and use makes advanced annotation accessible to a wider range of researchers.
TransAnnot is a valuable tool for accelerating biological discovery through efficient transcriptome analysis.