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TranscriptDB: a transcript-centric database to study eukaryotic transcript conservation and evolution.

Wend Yam D D Ouedraogo1, Aida Ouangraoua1

  • 1Department of Computer Science, Faculté des sciences, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada.

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|November 12, 2024
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Summary
This summary is machine-generated.

TranscriptDB is a new database for studying transcript conservation and evolution across eukaryotic gene families. It catalogs conserved transcripts and phylogenies for 317 species, aiding in understanding gene and transcript evolution.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Alternative splicing (AS) in eukaryotes produces multiple transcripts from single genes.
  • Existing databases lack comprehensive data on transcript conservation and evolution across species.
  • Identifying conserved transcripts aids in understanding homology, function, and phylogenetic relationships.

Purpose of the Study:

  • To develop TranscriptDB, a dedicated resource for studying transcript conservation and evolution within gene families.
  • To provide a catalog of conserved transcripts and phylogenies for multiple eukaryotic species.
  • To facilitate the exploration of gene and transcript evolution.

Main Methods:

  • Compiled conserved transcript data and phylogenies from Ensembl database version 111 for 317 eukaryotic species.
  • Developed a user-friendly web interface for browsing and querying the database.
  • Integrated web servers for analyzing user-submitted data and a REST API for programmatic access.

Main Results:

  • TranscriptDB offers an extensive catalog of conserved transcripts and phylogenies across 317 annotated eukaryotic species.
  • The database facilitates the study of gene and transcript evolution, including homology and phylogenetic reconstruction.
  • Accessible data includes a web interface, web servers, a REST API, and bulk download options.

Conclusions:

  • TranscriptDB addresses the gap in resources for studying transcript conservation and evolution.
  • The database provides valuable tools for researchers investigating eukaryotic gene and transcript evolution.
  • TranscriptDB is freely accessible, promoting broader research in evolutionary transcriptomics.