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Related Experiment Videos

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.

Scott Schwartz1, Laura Elnitski, Mei Li

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

Nucleic Acids Research
|June 26, 2003
PubMed
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The MultiPipMaker server rapidly aligns long genomic DNA sequences, aiding in the discovery of functional regulatory regions and confirming evolutionary relationships. This tool helps generate testable hypotheses about gene function and phylogeny.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Multiple sequence alignments are crucial for generating hypotheses about phylogenetic history and cellular function of genomic sequences.
  • Existing tools may lack the speed or sensitivity required for analyzing long genomic DNA sequences.

Purpose of the Study:

  • To introduce the MultiPipMaker server for rapid and sensitive alignment of multiple, long genomic DNA sequences.
  • To provide new tools for searching alignment outputs for conserved patterns and transcription factor binding sites.
  • To demonstrate the utility of MultiPipMaker in identifying and validating functional regulatory elements.

Main Methods:

  • The MultiPipMaker server aligns a reference sequence with secondary sequences (finished or draft).

Related Experiment Videos

  • Outputs include percent identity plots (MultiPip) and nucleotide-level multiple alignments.
  • New search tools identify conserved matches to patterns and position weight matrices for transcription factor binding sites.

    • Main Results:

    • MultiPipMaker provides fast and sensitive alignments of multiple, long genomic sequences.
    • The server successfully identified candidate regulatory regions in the WNT2 gene.
    • Transfection assays confirmed the functionality of the identified regulatory regions.
    • Alignment analysis supported phylogenetic inferences regarding equid and felid evolutionary relationships.

    Conclusions:

    • MultiPipMaker is an effective tool for analyzing genomic sequence alignments.
    • The server facilitates the discovery and functional validation of regulatory elements.
    • MultiPipMaker aids in phylogenetic analysis and hypothesis generation in genomics.