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Related Experiment Videos

Spidey: a tool for mRNA-to-genomic alignments.

S J Wheelan1, D M Church, J M Ostell

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. wheelan@ncbi.nlm.nih.gov

Genome Research
|November 3, 2001
PubMed
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We created Spidey, a fast computer program for aligning spliced sequences to genomes. It accurately handles noisy data like alternative splicing and errors, making it a reliable tool for genomic research.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Aligning complementary DNA (cDNA) or messenger RNA (mRNA) sequences to genomic DNA is crucial for gene identification and analysis.
  • Existing alignment tools may struggle with complexities such as alternative splicing, polymorphisms, sequencing errors, and evolutionary divergence.

Purpose of the Study:

  • To develop and evaluate a novel computer program, Spidey, for accurate and efficient spliced sequence alignment to genomic sequences.
  • To assess Spidey's performance in handling various data complexities and compare it with existing alignment tools.

Main Methods:

  • Development of a computer program utilizing local alignment algorithms and heuristics to achieve global spliced alignments.
  • Application of Spidey for aligning reference sequences to genomic sequences, including the draft human genome.

Related Experiment Videos

  • Utilizing Spidey for aligning mRNA sequences to gene clusters and cross-species genomic alignment (mouse mRNA to human genome).

    • Main Results:

    • Spidey demonstrates the ability to produce reliable spliced alignments rapidly.
    • The program effectively handles noisy sequence data, including alternative splicing, polymorphisms, sequencing errors, and evolutionary divergence.
    • Comparative analysis shows Spidey performs competitively against other spliced alignment programs within reasonable timeframes.

    Conclusions:

    • Spidey is a robust and efficient tool for spliced sequence alignment.
    • Its capability to manage data complexities makes it valuable for diverse genomic research applications.
    • Spidey offers a reliable and timely solution for aligning sequences to genomic data.