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GMAP: a genomic mapping and alignment program for mRNA and EST sequences.

Thomas D Wu1, Colin K Watanabe

  • 1Department of Bioinformatics Genentech, Inc., South San Francisco, CA 94080, USA. twu@gene.com

Bioinformatics (Oxford, England)
|February 25, 2005
PubMed
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The GMAP program accurately maps cDNA sequences to genomes, identifying splice sites with high precision and speed. This tool offers efficient batch processing and reliable gene structure generation, outperforming existing methods.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Existing methods for mapping cDNA to genomes have limitations in accuracy and speed.
  • Accurate gene structure identification is crucial for understanding gene function and regulation.

Purpose of the Study:

  • Introduce GMAP, a novel standalone program for efficient and accurate cDNA-to-genome mapping and alignment.
  • Evaluate GMAP's performance against established tools in terms of accuracy, speed, and gene structure prediction.

Main Methods:

  • Minimal sampling strategy for genomic mapping.
  • Oligomer chaining for approximate sequence alignment.
  • Dynamic programming (DP) for splice site detection and microexon identification.

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Main Results:

  • GMAP achieved over 99.3% accuracy in splice site identification on human mRNAs with mutations.
  • Demonstrated superior alignment quality compared to blat on human expressed sequence tags.
  • Exhibited comparable performance to GeneSeqer on Arabidopsis cDNAs.
  • Showcased a several-fold increase in processing speed over existing programs.

Conclusions:

  • GMAP provides a highly accurate and efficient solution for cDNA-to-genome mapping.
  • The program effectively handles sequence polymorphisms and errors without relying on probabilistic models.
  • GMAP offers a significant advancement in bioinformatics tools for genomic analysis.