Volume visualization of multiple alignment of large genomicDNA

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Description

Genomes of hundreds of species have been sequenced to date, and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. As a result, tools using 1D representations are incapable of providing informatory overview for extremely large data sets. We present ... continued below

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Shah, Nameeta; Dillard, Scott E.; Weber, Gunther H. & Hamann, Bernd July 25, 2005.

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Description

Genomes of hundreds of species have been sequenced to date, and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. As a result, tools using 1D representations are incapable of providing informatory overview for extremely large data sets. We present a technique to arrange 1D data in 3D space to allow us to apply state-of-the-art interactive volume visualization techniques for data exploration. We demonstrate our technique using multi-millions-basepair-long aligned DNA sequence data and compare it with traditional 1D line plots. The results show that our technique is superior in providing an overview of entire data sets. Our technique, coupled with 1D line plots, results in effective multi-resolution visualization of very large aligned sequence data sets.

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  • Report No.: LBNL--63126
  • Report No.: LBNL-55386
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 913175
  • Archival Resource Key: ark:/67531/metadc887169

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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  • July 25, 2005

Added to The UNT Digital Library

  • Sept. 22, 2016, 2:13 a.m.

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Shah, Nameeta; Dillard, Scott E.; Weber, Gunther H. & Hamann, Bernd. Volume visualization of multiple alignment of large genomicDNA, book, July 25, 2005; (digital.library.unt.edu/ark:/67531/metadc887169/: accessed December 16, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.