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

Scott Schwartz; Laura Elnitski; Mei Li; Matt Weirauch; Cathy Riemer; Arian Smit; Jim Thomas; Jeff Touchman; Bob Blakesley; Gerry Bouffard; Steve Beckstrom-Sternberg; Pam Thomas; Jenny McDowell; Baishali Maskeri; Nancy Hansen; Elliott Margulies; Eric D. Green; Ross C. Hardison; Webb Miller

doi:10.1093/nar/gkg579

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

Scott Schwartz, Laura Elnitski, Mei Li, Matt Weirauch, Cathy Riemer, Arian Smit, Jim Thomas, Jeff Touchman, Bob Blakesley, Gerry Bouffard, Steve Beckstrom-Sternberg, Pam Thomas, Jenny McDowell, Baishali Maskeri, Nancy Hansen, Elliott Margulies, Eric D. Green, Ross C. Hardison, Webb Miller

Biological Sciences

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192 Scopus citations

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.

Original language	English (US)
Pages (from-to)	3518-3524
Number of pages	7
Journal	Nucleic Acids Research
Volume	31
Issue number	13
DOIs	https://doi.org/10.1093/nar/gkg579
State	Published - Jul 1 2003

ASJC Scopus subject areas

Genetics

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Schwartz, S., Elnitski, L., Li, M., Weirauch, M., Riemer, C., Smit, A., Thomas, J., Touchman, J., Blakesley, B., Bouffard, G., Beckstrom-Sternberg, S., Thomas, P., McDowell, J., Maskeri, B., Hansen, N., Margulies, E., Green, E. D., Hardison, R. C., & Miller, W. (2003). MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Research, 31(13), 3518-3524. https://doi.org/10.1093/nar/gkg579

Schwartz, S, Elnitski, L, Li, M, Weirauch, M, Riemer, C, Smit, A, Thomas, J, Touchman, J, Blakesley, B, Bouffard, G, Beckstrom-Sternberg, S, Thomas, P, McDowell, J, Maskeri, B, Hansen, N, Margulies, E, Green, ED, Hardison, RC & Miller, W 2003, 'MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences', Nucleic Acids Research, vol. 31, no. 13, pp. 3518-3524. https://doi.org/10.1093/nar/gkg579

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title = "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.",

author = "Scott Schwartz and Laura Elnitski and Mei Li and Matt Weirauch and Cathy Riemer and Arian Smit and Jim Thomas and Jeff Touchman and Bob Blakesley and Gerry Bouffard and Steve Beckstrom-Sternberg and Pam Thomas and Jenny McDowell and Baishali Maskeri and Nancy Hansen and Elliott Margulies and Green, {Eric D.} and Hardison, {Ross C.} and Webb Miller",

note = "Funding Information: We thank Blair Hedges for advice on mammalian phylo-genetics. This work was supported by PHS grants HG02238 (to W.M.), DK27635 (to R.C.H.), and HG02325 (to L.E.). E.D.G. and the NISC Comparative Sequencing Program were supported by funds from the National Human Genome Research Institute. The following individuals were key contributors within the NISC Comparative Sequencing Program: Jim Thomas (BAC isolation and mapping); Jeff Touchman and Bob Blakesley (BAC sequencing); Gerry Bouffard, Steve Beckstrom-Sternberg, Pam Thomas, Jenny McDowell, Baishali Maskeri, Nancy Hansen, and Elliott Margulies (computational analyses).",

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AU - Schwartz, Scott

AU - Elnitski, Laura

AU - Li, Mei

AU - Weirauch, Matt

AU - Riemer, Cathy

AU - Smit, Arian

AU - Thomas, Jim

AU - Touchman, Jeff

AU - Blakesley, Bob

AU - Bouffard, Gerry

AU - Beckstrom-Sternberg, Steve

AU - Thomas, Pam

AU - McDowell, Jenny

AU - Maskeri, Baishali

AU - Hansen, Nancy

AU - Margulies, Elliott

AU - Green, Eric D.

AU - Hardison, Ross C.

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N2 - 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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MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences

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