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Related Experiment Videos

MultiPipMaker: comparative alignment server for multiple DNA sequences.

Laura Elnitski1, Cathy Riemer, Richard Burhans

  • 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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MultiPipMaker is a web tool for aligning multiple genomic sequences and identifying conserved regions. It offers nucleotide-level alignments or identity plots with customizable annotations for biological insights.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Multiple sequence alignment is crucial for identifying conserved regions and understanding evolutionary relationships.
  • Existing tools may have limitations in handling very long genomic sequences or providing flexible visualization options.

Purpose of the Study:

  • To describe the functionality and usage of the MultiPipMaker World Wide Web server.
  • To explain the interpretation of MultiPipMaker's output files and associated tools.

Main Methods:

  • Utilizing the MultiPipMaker web server for aligning up to 20 long genomic sequences.
  • Exploring output options including nucleotide-level multiple alignments and pairwise percent identity plots.
  • Implementing user-specified annotations for genomic features with interactive links.

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Main Results:

  • Successful alignment of multiple, long genomic sequences.
  • Generation of detailed nucleotide-level alignments and visual percent identity plots.
  • Inclusion of customizable annotations for enhanced biological interpretation.

Conclusions:

  • MultiPipMaker provides a versatile platform for genomic sequence analysis and conservation visualization.
  • The server facilitates the identification of functionally important regions across multiple genomes.
  • User-friendly features and flexible output formats enhance its utility for researchers.