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PipMaker--a web server for aligning two genomic DNA sequences.

S Schwartz1, Z Zhang, K A Frazer

  • 1Department of Computer Science and Engineering, The Pennsylvania State University, University Park 16802, USA.

Genome Research
|April 26, 2000
PubMed
Summary
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PipMaker is a web tool for comparing DNA sequences to find conserved segments. It generates visual plots to highlight similarities and aids in analyzing genomic data from related species.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Comparing long DNA sequences is crucial for understanding genome evolution and function.
  • Identifying conserved segments aids in locating functionally important genomic regions.

Purpose of the Study:

  • To introduce PipMaker, a World-Wide Web site for comparing two long DNA sequences.
  • To provide informative, high-resolution displays of DNA sequence alignments and conserved segments.

Main Methods:

  • PipMaker utilizes percent identity plots (pip) to visualize sequence similarity.
  • The tool supports analysis of both finished and unfinished genomic sequences.
  • It offers comparative plots similar to dot plots for genomic segment locations.

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Main Results:

  • PipMaker effectively identifies conserved segments between two DNA sequences.
  • The percent identity plot (pip) provides a compact and understandable display of sequence alignments.
  • The web site facilitates the detection of features like protein-coding regions and cis-regulatory elements.

Conclusions:

  • PipMaker is a valuable resource for comparative genomics across diverse species.
  • The tool aids in the discovery of functional genomic elements, even in distantly related species.
  • PipMaker supports the analysis of complex genomic data, including unoriented and unordered contigs.