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Related Experiment Videos

PipMaker: a World Wide Web server for genomic sequence alignments.

Laura Elnitski1, Cathy Riemer, Scott Schwartz

  • 1The Pennsylvania State University, University Park, Pennsylvania, USA.

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
Summary
This summary is machine-generated.

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PipMaker is a web tool that compares genomic sequences to find conserved segments using percent identity plots (pip). It offers an efficient way to visualize sequence alignments and identify similarities between species, like human and mouse.

Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative genomics

Background:

  • Comparing long genomic sequences is crucial for understanding genome evolution and function.
  • Identifying conserved segments aids in pinpointing functionally important regions across species.
  • Existing methods may lack efficiency or user-friendly output for large-scale sequence comparisons.

Purpose of the Study:

  • To describe the PipMaker web server for comparing genomic sequences.
  • To explain the interpretation of PipMaker's output, particularly the percent identity plot (pip).
  • To highlight PipMaker's utility in identifying conserved segments between two long genomic sequences.

Main Methods:

  • Utilizes the PipMaker web server for sequence comparison.
  • Employs the blastz alignment program with default parameters optimized for human-mouse alignments.

Related Experiment Videos

  • Generates percent identity plots (pips) to visualize sequence similarity and conservation.

    • Main Results:

    • PipMaker efficiently aligns genomic sequences, producing interpretable percent identity plots (pips).
    • Each pip displays the position and degree of similarity for aligning segments.
    • Optional annotations enhance the interpretation of alignment results.

    Conclusions:

    • PipMaker provides an effective and user-friendly method for identifying conserved segments in genomic sequences.
    • The percent identity plot (pip) offers a clear visualization of sequence similarity.
    • The tool is particularly useful for comparative genomics studies, such as human-mouse alignments.