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A quantitative comparison of DNA sequence assembly programs

M J Miller1, J I Powell

  • 1Laboratory of Experimental Carcinogenesis, National Cancer Institute, Bethesda, MD 20892, USA. mark@helix.nih.gov

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|January 1, 1994
PubMed
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This study evaluated 11 DNA sequence assembly programs, identifying GCG, FAB, and AutoAssembler as top performers for accuracy and reproducibility in assembling DNA fragments. Sequencher also offered superior sequence editing capabilities.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Accurate DNA sequence assembly is crucial for genomic research.
  • Evaluating the performance of various sequence assembly programs is essential for optimizing research workflows.

Purpose of the Study:

  • To compare the accuracy and reproducibility of 11 DNA sequence assembly programs.
  • To assess the impact of sequence errors and fragment order on assembly quality.
  • To evaluate the sequence editing capabilities of the compared programs.

Main Methods:

  • A controlled study using fragments of the rat multidrug resistance (RATMDRM) gene sequence.
  • Introduction of random errors (miss-identified, missed, duplicated bases) at varying percentages (0-15%).
  • Evaluation of assembly quality by comparing assembled sequences to the original sequence and assessing reproducibility.

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Main Results:

  • Programs were categorized into three groups based on performance: high accuracy/reproducibility (GCG, FAB, AutoAssembler), intermediate (Sequencher, AssemblyLIGN, XBAP, SeqMan, AutoAssembler with external processor), and lower (GeneWorks, GENeration, PC/Gene).
  • Sequence order did not significantly affect final assembly quality.
  • Sequencher demonstrated a well-designed editor for rapid examination and correction of assembly errors, with five programs supporting trace file editing.

Conclusions:

  • GCG, FAB, and AutoAssembler are recommended for accurate and reproducible DNA sequence assembly.
  • Sequencher provides advanced editing features crucial for refining assembled sequences.
  • The choice of assembly program impacts research efficiency and data reliability.