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MultiPipMaker: a comparative alignment server for multiple DNA sequences.

Laura Elnitski1, Richard Burhans1, Cathy Riemer1

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

Current Protocols in Bioinformatics
|June 4, 2010
PubMed
Summary
This summary is machine-generated.

MultiPipMaker is a web server for aligning multiple DNA sequences and identifying conserved regions. It offers nucleotide-level alignments and conservation plots for genomic data analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

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

Purpose of the Study:

  • To introduce and describe the MultiPipMaker web server for multiple DNA sequence alignment.
  • To explain the functionality, output, and supporting tools of the MultiPipMaker server.

Main Methods:

  • Utilizes a web server accessible via http://www.bx.psu.edu.
  • Accepts up to 20 very long genomic sequences for alignment.
  • Provides options for nucleotide-level multiple alignment and pairwise percent identity plots.
  • Supports user-specified annotations for genomic features and regions.

Main Results:

  • The MultiPipMaker server enables the alignment of extensive genomic sequences.
  • It generates detailed nucleotide-level alignments and visualizes conservation patterns.
  • User-defined annotations can be integrated, with interactive links to further information.
  • Handles fragmented, unordered, and unoriented input sequences.

Conclusions:

  • MultiPipMaker offers a powerful and flexible tool for comparative genomics.
  • The server facilitates the identification and analysis of conserved DNA elements across multiple genomes.
  • Its features support in-depth investigation of genomic sequence conservation and annotation.