MultiPipMaker and Supporting Tools: Alignments and Analysis of Multiple Genomic DNA Sequences

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Jun 26

PMID 12824357

Citations 106

Authors

Scott Schwartz

Laura Elnitski

Mei Li

Matt Weirauch

Cathy Riemer

Arian Smit

Eric D Green

Ross C Hardison

Webb Miller

Affiliations

Soon will be listed here.

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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References

Gottgens B, Barton L, GILBERT J, Bench A, Sanchez M, Bahn S . Analysis of vertebrate SCL loci identifies conserved enhancers. Nat Biotechnol. 2000; 18(2):181-6. DOI: 10.1038/72635. View

Wasserman W, Palumbo M, Thompson W, Fickett J, Lawrence C . Human-mouse genome comparisons to locate regulatory sites. Nat Genet. 2000; 26(2):225-8. DOI: 10.1038/79965. View

Loots G, Locksley R, Blankespoor C, Wang Z, Miller W, Rubin E . Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science. 2001; 288(5463):136-40. DOI: 10.1126/science.288.5463.136. View

Schwartz S, Zhang Z, Frazer K, Smit A, Riemer C, Bouck J . PipMaker--a web server for aligning two genomic DNA sequences. Genome Res. 2000; 10(4):577-86. PMC: 310868. DOI: 10.1101/gr.10.4.577. View

Dubchak I, Brudno M, Loots G, Pachter L, Mayor C, Rubin E . Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 2000; 10(9):1304-6. PMC: 310906. DOI: 10.1101/gr.142200. View

Mayor C, Brudno M, Schwartz J, Poliakov A, Rubin E, Frazer K . VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 2001; 16(11):1046-7. DOI: 10.1093/bioinformatics/16.11.1046. View

Pennacchio L, Rubin E . Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet. 2001; 2(2):100-9. DOI: 10.1038/35052548. View

Murphy W, Eizirik E, OBrien S, Madsen O, Scally M, Douady C . Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001; 294(5550):2348-51. DOI: 10.1126/science.1067179. View

Berman B, Nibu Y, Pfeiffer B, Tomancak P, Celniker S, Levine M . Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A. 2002; 99(2):757-62. PMC: 117378. DOI: 10.1073/pnas.231608898. View

10.

Thomas J, Touchman J . Vertebrate genome sequencing: building a backbone for comparative genomics. Trends Genet. 2002; 18(2):104-8. DOI: 10.1016/s0168-9525(02)02599-4. View

11.

Chiaromonte F, Yap V, Miller W . Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002; :115-26. DOI: 10.1142/9789812799623_0012. View

12.

Waterston R, Lindblad-Toh K, Birney E, Rogers J, Abril J, Agarwal P . Initial sequencing and comparative analysis of the mouse genome. Nature. 2002; 420(6915):520-62. DOI: 10.1038/nature01262. View

13.

Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R . TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 2003; 31(1):374-8. PMC: 165555. DOI: 10.1093/nar/gkg108. View

14.

Frazer K, Elnitski L, Church D, Dubchak I, Hardison R . Cross-species sequence comparisons: a review of methods and available resources. Genome Res. 2003; 13(1):1-12. PMC: 430969. DOI: 10.1101/gr.222003. View

15.

Hardison R, Roskin K, Yang S, Diekhans M, Kent W, Weber R . Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 2003; 13(1):13-26. PMC: 430971. DOI: 10.1101/gr.844103. View

16.

Elnitski L, Hardison R, Li J, Yang S, Kolbe D, Eswara P . Distinguishing regulatory DNA from neutral sites. Genome Res. 2003; 13(1):64-72. PMC: 430974. DOI: 10.1101/gr.817703. View

17.

Schwartz S, Kent W, Smit A, Zhang Z, Baertsch R, Hardison R . Human-mouse alignments with BLASTZ. Genome Res. 2003; 13(1):103-7. PMC: 430961. DOI: 10.1101/gr.809403. View

18.

Brudno M, Do C, Cooper G, Kim M, Davydov E, Green E . LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 2003; 13(4):721-31. PMC: 430158. DOI: 10.1101/gr.926603. View

19.

Kimura M . Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature. 1977; 267(5608):275-6. DOI: 10.1038/267275a0. View

20.

Efstratiadis A, Posakony J, Maniatis T, Lawn R, OConnell C, Spritz R . The structure and evolution of the human beta-globin gene family. Cell. 1980; 21(3):653-68. DOI: 10.1016/0092-8674(80)90429-8. View