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The TIGR Plant Transcript Assemblies database.

Kevin L Childs1, John P Hamilton, Wei Zhu

  • 1The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

Nucleic Acids Research
|November 8, 2006
PubMed
Summary
This summary is machine-generated.

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The TIGR Plant Transcript Assemblies (TA) database provides curated plant transcript data from public sequences. It aids researchers by offering assembled sequences and functional annotations for 215 plant species.

Area of Science:

  • Bioinformatics
  • Genomics
  • Plant Science

Background:

  • Publicly available expressed sequence data is crucial for understanding plant genomes.
  • Existing databases may lack comprehensive transcript assemblies or functional annotations.

Purpose of the Study:

  • To describe the TIGR Plant Transcript Assemblies (TA) database, a resource for plant transcript data.
  • To detail the methods used for constructing and annotating transcript assemblies.
  • To highlight the accessibility and scope of the database.

Main Methods:

  • Collected expressed sequence tags (ESTs) and cDNAs from NCBI GenBank.
  • Clustered sequences using TGICL, Megablast, and CAP3 for transcript assembly.
  • Annotated assemblies using the UniProt Reference Clusters (UniRef100) protein database.

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Main Results:

  • The TA database contains transcript assemblies for 215 plant species.
  • Functional annotation and transcription orientation are provided for each assembly.
  • Data is accessible via web interfaces and FTP downloads with search capabilities.

Conclusions:

  • The TA database is a valuable resource for plant genomics research.
  • It provides a comprehensive and accessible collection of plant transcript assemblies.
  • The database facilitates functional annotation and comparative genomics studies.