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[Construction of standard human transcript dataset based on RefSeq and human genome sequence database].

Zhi-Feng Li1, Yu-Jian Li, Dong-Sheng Zhao

  • 1Beijing Institute of Radiation Medicine, Beijing 100850, China. lizf@bmi.ac.cn

Yi Chuan = Hereditas
|March 23, 2006
PubMed
Summary

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This study defines a standard transcript based on genomic DNA mapping to improve the NCBI RefSeq database. A large-scale analysis identified high-quality human transcripts for future genetic research.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Context:

  • The NCBI RefSeq database aims for non-redundant DNA, RNA, and protein sequences.
  • Polymorphisms and varying experimental quality can introduce errors into RefSeq.
  • A standardized approach is needed to ensure transcript accuracy.

Purpose:

  • To define and identify "standard transcripts" by mapping RefSeq records to human genome sequences.
  • To assess the quality and accuracy of human RefSeq records.
  • To provide a high-quality reference dataset for further genetic analysis.

Summary:

  • A novel "standard transcript" concept was established, requiring perfect exon-level mapping to genomic DNA.
  • BLAT, Sim4, and EIparser were used to analyze human RefSeq records against the human genome.

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  • 9,771 RefSeq records mapped perfectly, 10,943 were revised, and 2,879 were flagged as potentially erroneous.

    • Impact:

    • Provides a curated, high-quality human reference dataset for bioinformatics and experimental studies.
    • Facilitates accurate analysis of human gene polymorphism and mutation studies.
    • Establishes criteria for transcript standardization in genomic databases.