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Related Experiment Videos

Bridging expressed sequence alignments through targeted cDNA sequencing.

Hanqing Xie1, Alex Diber, Sarah Pollock

  • 1Compugen, Inc., 7 Center Drive, Suite 9, Jamesburg, NJ 08831, USA. han@cgen.com

Genomics
|March 19, 2004
PubMed
Summary
This summary is machine-generated.

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Identifying complete gene sets in genomes is challenging. This study introduces targeted cDNA sequencing to bridge sequence alignments, efficiently characterizing novel and incomplete genes.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Identifying the complete set of genes within a genome is a significant challenge in genomic research.
  • Aligning expressed sequences (RNA and EST) with genomic sequences aids gene characterization, but often results in numerous alignments needing consolidation.
  • High-throughput EST sequencing is inefficient for closing alignment gaps due to its non-selective nature.

Purpose of the Study:

  • To develop and validate a novel approach for bridging sequence alignments using targeted cDNA sequencing.
  • To efficiently characterize novel or incomplete genes by generating overlapping sequences.

Main Methods:

  • Alignment of human expressed sequences (GenBank v124) with genomic sequences (NCBI build 24) using the LEADS software system.

Related Experiment Videos

  • Selection of 948 alignment pairs based on EST clone information and/or homology to known proteins.
  • Application of reverse transcriptase PCR and sequencing to generate overlapping sequences for selected alignment pairs.

    • Main Results:

    • Successful sequencing of 363 out of 948 targeted alignment pairs.
    • Characterization of over 60 novel or incomplete human genes in UniGene build 153.
    • Demonstration that the integrated strategy efficiently generates overlapping sequences.

    Conclusions:

    • An integrated strategy combining computational prediction and targeted experimental cDNA sequencing is effective for full genome characterization.
    • This approach efficiently bridges sequence alignment gaps, enabling the identification of complete gene structures.
    • The method significantly advances the ability to identify and characterize genes within complex genomes.