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Nucleic acids research2003; 31(13); 3518-3524; doi: 10.1093/nar/gkg579

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

Abstract: Analysis of multiple sequence alignments can generate important, testable hypotheses about the phylogenetic history and cellular function of genomic sequences. We describe the MultiPipMaker server, which aligns multiple, long genomic DNA sequences quickly and with good sensitivity (available at http://bio.cse.psu.edu/ since May 2001). Alignments are computed between a contiguous reference sequence and one or more secondary sequences, which can be finished or draft sequence. The outputs include a stacked set of percent identity plots, called a MultiPip, comparing the reference sequence with subsequent sequences, and a nucleotide-level multiple alignment. New tools are provided to search MultiPipMaker output for conserved matches to a user-specified pattern and for conserved matches to position weight matrices that describe transcription factor binding sites (singly and in clusters). We illustrate the use of MultiPipMaker to identify candidate regulatory regions in WNT2 and then demonstrate by transfection assays that they are functional. Analysis of the alignments also confirms the phylogenetic inference that horses are more closely related to cats than to cows.
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Publication Date: 2003-06-26 PubMed ID: 12824357PubMed Central: PMC168985DOI: 10.1093/nar/gkg579Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article describes the MultiPipMaker server, a tool for aligning and analyzing multiple, long genomic DNA sequences. The information generated can lead to hypotheses about genetic history and microscopic functionality of these sequences. Furthermore, several examples of its application, such as the identification of potential regulatory regions in WNT2 and commencement of phylogenetic inference, are provided.

Understanding MultiPipMaker and its Features

  • The study introduces MultiPipMaker, an online server that performs the alignment of multiple, long genomic DNA sequences promptly with high sensitivity. It does this by matching a continuous reference sequence with one or more secondary sequences. These secondary sequences could either be finished or draft sequences.
  • Some of the outputs provided by the server include MultiPip, a stacked set of percent identity plots that enables comparison between the reference sequence and subsequent sequences. Also, it provides a nucleotide-level multiple alignment.

Additional Tools and Their Functions

  • In addition to these features, new tools have been incorporated to increase the software’s functionality. For instance, a tool has been added to search the output of MultiPipMaker for conserved matches to user-specified patterns.
  • Additionally, the possibility of searching for conserved matches to position weight matrices that detail transcription factor binding sites is also included. These sites can be either individually or in clusters.

Applications of MultiPipMaker

  • MultiPipMaker can be used to identify potential regulatory regions, which can play a crucial role in gene expression. In their study, the authors used this tool to identify such regions in the WNT2 gene and performed transfection assays to establish their functionality.
  • The ability of the software to perform multiple sequence alignments and analyses also facilitates phylogenetic inference. This application was demonstrated by confirming that horses share a closer genetic relation to cats than to cows.

Cite This Article

APA
Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A, Green ED, Hardison RC, Miller W. (2003). MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res, 31(13), 3518-3524. https://doi.org/10.1093/nar/gkg579

Publication

Nucleic acids research
ISSN: 1362-4962
NlmUniqueID: 0411011
Country: England
Language: English
Volume: 31
Issue: 13
Pages: 3518-3524

Researcher Affiliations

Schwartz, Scott
  • Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
Elnitski, Laura
    Li, Mei
      Weirauch, Matt
        Riemer, Cathy
          Smit, Arian
            Green, Eric D
              Hardison, Ross C
                Miller, Webb

                  MeSH Terms

                  • Algorithms
                  • Animals
                  • Binding Sites
                  • Cats
                  • Genomics / methods
                  • Horses / classification
                  • Horses / genetics
                  • Internet
                  • Phylogeny
                  • Proto-Oncogene Proteins / genetics
                  • Regulatory Sequences, Nucleic Acid
                  • Sequence Alignment / methods
                  • Sequence Analysis, DNA / methods
                  • Software
                  • Transcription Factors / metabolism
                  • Wnt2 Protein

                  Grant Funding

                  • HG02238 / NHGRI NIH HHS
                  • DK27635 / NIDDK NIH HHS
                  • F32 HG002325 / NHGRI NIH HHS
                  • HG02325 / NHGRI NIH HHS
                  • R01 HG002238 / NHGRI NIH HHS

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