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Aligning a DNA sequence with a protein sequence

Z Zhang1, W R Pearson, W Miller

  • 1Department of Computer Science and Engineering, The Pennsylvania State University, University Park 16802, USA. zzhang@galapagos.cse.psu.edu

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 1, 1997
PubMed
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We developed new algorithms for aligning DNA and protein sequences, handling frameshift errors in cDNA. These methods improve comparisons with protein databases, enhancing sequence analysis tools like FASTA.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate alignment of DNA and protein sequences is crucial for understanding gene and protein function.
  • Existing methods may struggle with sequencing errors and specific sequence types like cDNA.

Purpose of the Study:

  • To develop and present novel algorithms for DNA-protein sequence alignment.
  • To address challenges posed by frameshift errors in DNA sequences during alignment.
  • To enhance the capabilities of sequence analysis tools for biological research.

Main Methods:

  • Development of several algorithms for DNA-protein sequence alignment.
  • Accounting for frameshift errors but explicitly excluding introns in DNA sequences.
  • Verification of conditions for the equivalence of different alignment definitions.

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  • Implementation of efficient techniques for practical application.

    • Main Results:

    • Algorithms are particularly suitable for aligning error-prone cDNA sequences with protein databases.
    • Optimal alignments are computed based on multiple definitions of DNA-protein alignment.
    • Efficient implementation techniques are described for practical use.
    • Successful integration of these algorithms into the FASTA sequence searching program.

    Conclusions:

    • The developed algorithms provide robust solutions for DNA-protein sequence alignment, especially with cDNA.
    • The methods effectively handle frameshift errors, improving alignment accuracy.
    • The integration into FASTA enhances its utility for biological sequence database searching.