MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences

Laura Elnitski1, Richard Burhans1, Cathy Riemer1, Ross Hardison1, Webb Miller1

1 The Pennsylvania State University, University Park, Pennsylvania
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 10.4
DOI:  10.1002/0471250953.bi1004s30
Online Posting Date:  June, 2010
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The MultiPipMaker World Wide Web server ( provides a tool for aligning multiple DNA sequences and visualizing regions of conservation among them. This unit describes its use and gives an explanation of the resulting output files and supporting tools. Features provided by the server include alignment of up to 20 very long genomic sequences, output choices of a true, nucleotide‐level multiple alignment and/or stacked, pairwise percent identity plots, and support for user‐specified annotations of genomic features and arbitrary regions, with clickable links to additional information. Input sequences other than the reference can be fragmented, unordered, and unoriented. Curr. Protoc. Bioinform. 30:10.4.1‐10.4.14. © 2010 by John Wiley & Sons, Inc.

Keywords: multiple alignment; percent identity plot; genomic analysis; conserved non‐coding sequences

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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: MultiPipMaker: Multiple Alignment Server
  • Support Protocol 1: Installing and Using Stand‐Alone refine and single_cov Programs
  • Support Protocol 2: Using PipHelper to Prepare MultiPipMaker Input Files from Data in the UCSC Genome Browser
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

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   Elnitski, L., Hardison, R.C., Li, J., Yang, S., Kolbe, D., Eswara, P., O'Connor, M.J., Schwartz, S., Miller, W., and Chiaromonte, F. 2003. Distinguishing regulatory DNA from neutral sites. Genome Res. 13:64‐72.
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   Schwartz, S., Elnitski, L., Li, M., Weirauch, M., Riemer, C., Smit, A., Green, E.D., Hardison, R.C., Miller, W., and NISC Comparative Sequencing Program. 2003a. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31:3518‐3524.
   Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D, and Miller, W. 2003b. Human mouse alignments with BLASTZ. Genome Res. 13:103‐107.
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   Stojanovic, N., Florea, L., Riemer, C., Gumucio, D., Slightom, J., Goodman, M., Miller, W., and Hardison, R. 1999. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Res. 27:3899‐3910.
   Thomas, J.W., Touchman, J.W., Blakesley, R.W., Bouffard, G.G., Beckstrom‐Sternberg, S.M., Margulies, E.H., Blanchette, M., Siepel, A.C., Thomas, P.J., McDowell, J.C., Maskeri, B., Hansen, N.F., Schwartz, M.S., Weber, R.J., Kent, W.J., Karolchik, D., Bruen, T.C., Bevan, R., Cutler, D.J., Schwartz, S., Elnitski, L., Idol, J.R., Prasad, A.B., Lee‐Lin, S.Q., Maduro, V.V., Summers, T.J., Portnoy, M.E., Dietrich, N.L., Akhter, N., Ayele, K., Benjamin, B., Cariaga, K., Brinkley, C.P., Brooks, S.Y., Granite, S., Guan, X., Gupta, J., Haghighi, P., Ho, S.L., Huang, M.C., Karlins, E., Laric, P.L., Legaspi, R., Lim, M.J., Maduro, Q.L., Masiello, C.A., Mastrian, S.D., McCloskey, J.C., Pearson, R., Stantripop, S., Tiongson, E.E., Tran, J.T., Tsurgeon, C., Vogt, J.L., Walker, M.A., Wetherby, K.D., Wiggins, L.S., Young, A.C., Zhang, L.H., Osoegawa, K., Zhu, B., Zhao, B., Shu, C.L., De Jong, P.J., Lawrence, C.E., Smit, A.F., Chakravarti, A., Haussler, D., Green, P., Miller, W., and Green, E.D. 2003. Comparative analyses of multi‐species sequences from targeted genomic regions. Nature 424:788‐793.
   Tufarelli, C., Hardison, R., Miller, W., Hughes, J., Clark, K., Ventress, N., Frischauf, A.M., and Higgs, D.R. 2004. Comparative analysis of the alpha‐like globin clusters in mouse, rat, and human chromosomes indicates a mechanism underlying breaks in conserved synteny. Genome Res. 14:623‐630.
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Key References
   Schwartz et al., 2000. See above.
  Describes the PipMaker server. PipMaker computes and displays pairwise alignments whereas MultiPipMaker computes and displays multiple sequence alignments.
   Schwartz et al., 2003a. See above.
  Describes the MultiPipMaker server and supporting tools.
Internet Resources
  Links to alignment programs including PipMaker and MultiPipMaker, software, publications, example pages, and instructions for use of the tools and the server.
  Home page for the UCSC Genome Browser.
  Home page for downloading Adobe Reader.
  Home page for the GNUzip software package.
  Entrez Nucleotide Web site containing sequenced DNA from numerous sources.
  Entrez Gene Web site containing annotations of genes and links to related resources.
  PubMed Web site: repository of published scientific literature.
  ENCODE Project homepage. Links to sequences and general information about the project.
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