Visualizing genomes: Techniques and challenges

Nature Methods

Volumn 7, Issue 3, 2010, Pages S1-S11

  Nielsen, Cydney B ^a   Cantor, Michael ^b   Dubchak, Inna ^b,c   Gordon, David ^d   Wang, Ting ^e  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

^e WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPARATIVE GENE MAPPING; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER AIDED DESIGN; COMPUTER PROGRAM; DATA ANALYSIS; GENE EXPRESSION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC IDENTIFICATION; GENETIC VARIABILITY; GENOMICS; GENOTYPE; HIGH THROUGHPUT SCREENING; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SYNTENY; TRANSCRIPTION REGULATION; WEB BROWSER;

COMPUTER GRAPHICS; GENOME; IMAGE PROCESSING, COMPUTER-ASSISTED;

EID: 77649253051     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.1422     Document Type: Review

References (88)

1. Pop, M. Genome assembly reborn: Recent computational challenges. Brief. Bioinform. 10, 354-366 (2009).
2. Flicek, P. & Birney, E. Sense from sequence reads: Methods for alignment and assembly. Nat. Methods 6 (suppl.), S6-S12 (2009).
3. Gordon, D., Abajian, C. & Green, P. Consed: A graphical tool for sequence finishing. Genome Res. 8, 195-202 (1998). a widely used finishing tool that was the first to use error probabilities as an objective criterion to guide the finishing process.
4. Ewing, B., Hillier, L., Wendl, M.C. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175-185 (1998).
5. Ewing, B. & Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194 (1998).
6. Schatz, M.C., Phillippy, A.M., Shneiderman, B. & Salzberg, S.L. Hawkeye: An interactive visual analytics tool for genome assemblies. Genome Biol. 8, R34 (2007).
7. Salzberg, S.L., Church, D., DiCuccio, M., Yaschenko, E. & Ostell, J. The Genome Assembly Archive: A new public resource. PLoS Biol. 2, E285 (2004).
8. Li, H. et al. The Sequence Alignment/Map (SAM) format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
9. Mardis, E.R. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9, 387-402 (2008).
10. Turner, D.J., Keane, T.M., Sudbery, I. & Adams, D.J. Next-generation sequencing of vertebrate experimental organisms. Mamm. Genome 20, 327-338 (2009).
11. Gordon, D., Desmarais, C. & Green, P. Automated finishing with autofinish. Genome Res. 11, 614-625 (2001).
12. Dear, S. & Staden, R. A sequence assembly and editing program for efficient management of large projects. Nucleic Acids Res. 19, 3907-3911 (1991).
13. Bonfield, J.K., Smith, K.F. & Staden, R. A new DNA sequence assembly program. Nucleic Acids Res. 23, 4992-4999 (1995).one of the first and a widely used finishing tool with an interactive graphical user interface and sequence editing capabilities. An updated version (Gap5) is designed to handle NGs data.
14. Burland, T.G. DNASTAR’s Lasergene sequence analysis software. Methods Mol. Biol. 132, 71-91 (2000).
15. Parsons, J.D. Miropeats: Graphical DNA sequence comparisons. Comput. Appl. Biosci. 11, 615-619 (1995).
16. Medvedev, P., Stanciu, M. & Brudno, M. Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods 6 (suppl.), S13-S20 (2009).
17. Huang, W. & Marth, G. EagleView: A genome assembly viewer for next-generation sequencing technologies. Genome Res. 18, 1538-1543 (2008).
18. Bao, H. et al. MapView: Visualization of short reads alignment on a desktop computer. Bioinformatics 25, 1554-1555 (2009).
19. Manske, H. & Kwiatkowski, D. LookSeq: A browser-based viewer for deep sequencing data. Genome Res. 19, 2125-2132 (2009).
20. Kim, P.-G., Cho, H.-G. & Park, K. A scaffold analysis tool using mate-pair information in genome sequencing. J. Biomed. Biotechnol. 2008, 675741 (2008).
21. Zerbino, D.R. & Birney, E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008).
22. Chaisson, M.J. & Pevzner, P.A. Short read fragment assembly of bacterial genomes. Genome Res. 18, 324-330 (2008).
23. Hernandez, D., Frangois, P., Farinelli, L., Osteras, M. & Schrenzel, J. De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Res. 18, 802-809 (2008).
24. MacCallum, I. et al. ALLPATHS 2: Small genomes assembled accurately and with high continuity from short paired reads. Genome Biol. 10, R103 (2009).
25. Nielsen, C.B., Jackman, S.D., Birol, I. & Jones, S.J. ABySS-Explorer: Visualizing genome sequence assemblies. IEEE Trans. Vis. Comput. Graph. 15, 881-888 (2009).
26. C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282, 2012-2018 (1998).
27. Eeckman, F.H. & Durbin, R. ACeDB and macace. Methods Cell Biol. 48, 583-605 (1995).
28. Stein, L.D. et al. The generic genome browser: A building block for a model organism system database. Genome Res. 12, 1599-1610 (2002). The Generic Model organism Database project is the most widely used framework for developing software tools to support genome analysis and curation. Three synteny-specific tools have been developed within the GMoD framework: synBrowse, synview and gBrowsesyn.
29. Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
30. Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002). widely used genome browser with user-friendly web interface and capability to display third party data.
31. Birney, E., Bateman, A., Clamp, M.E. & Hubbard, T.J. Mining the draft human genome. Nature 409, 827-828 (2001).
32. Stalker, J. et al. The Ensembl web site: Mechanics of a genome browser. Genome Res. 14, 951-955 (2004).
33. Wheeler, D.L. et al. Database resources of the National Center for Biotechnology. Nucleic Acids Res. 31, 28-33 (2003).
34. Cline, M.S. & Kent, W.J. Understanding genome browsing. Nat. Biotechnol. 27, 153-155 (2009).
35. Furey, T.S. Comparison of human (and other) genome browsers. Hum. Genomics 2, 266-270 (2006).
36. Giardine, B. et al. Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15, 1451-1455 (2005).
37. ENCODE ProjectConsortium, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007).
38. Cancer Genome Atlas Research Network Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
39. Skinner, M.E., Uzilov, A.V., Stein, L.D., Mungall, C.J. & Holmes, I.H. JBrowse: A next-generation genome browser. Genome Res. 19, 1630-1638 (2009).
40. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
41. Yates, T., Okoniewski, M.J. & Miller, C.J. X: Map: Annotation and visualization of genome structure for Affymetrix exon array analysis. Nucleic Acids Res. 36 Database issue, D780-D786 (2008).
42. Arakawa, K. et al. Genome Projector: Zoomable genome map with multiple views. BMC Bioinformatics 10, 31 (2009).
43. Zhu, J. et al. The UCSC Cancer Genomics Browser. Nat. Methods 6, 239-240 (2009).
44. Anders, S. Visualization of genomic data with the Hilbert curve. Bioinformatics 25, 1231-1235 (2009).
45. Homer, N. et al. Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet. 4, e1000167 (2008).
46. Ureta-Vidal, A., Ettwiller, L. & Birney, E. Comparative genomics: Genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4, 251-262 (2003).
47. Freeling, M. & Subramaniam, S. Conserved noncoding sequences (CNSs) in higher plants. Curr. Opin. Plant Biol. 12, 126-132 (2009).
48. Drosophila 12 Genomes Consortium. et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218 (2007).
49. Richter, D.C., Schuster, S.C. & Huson, D.H. OSLay: Optimal syntenic layout of unfinished assemblies. Bioinformatics 23, 1573-1579 (2007).
50. Schwartz, S. et al. Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107 (2003).
51. Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715 (2004).
52. Brudno, M. et al. Glocal alignment: Finding rearrangements during alignment. Bioinformatics 19 (suppl. 1), i54-i62 (2003).
53. Dewey, C.N. Aligning multiple whole genomes with Mercator and MAVID. Methods Mol. Biol. 395, 221-236 (2007).
54. Darling, A.C.E., Mau, B., Blattner, F.R. & Perna, N.T. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403 (2004).
55. Dubchak, I., Poliakov, A., Kislyuk, A. & Brudno, M. Multiple whole-genome alignments without a reference organism. Genome Res. 19, 682-689 (2009).
56. Frazer, K.A., Pachter, L., Poliakov, A., Rubin, E.M. & Dubchak, I., VISTA: Computational tools for comparative genomics. Nucleic Acids Res. 32 (Web Server issue), W273-W279 (2004).A comprehensive suite of programs and databases for comparative analysis of genomic sequences. whole-genome alignments of many species from different taxa (vertebrates to prokaryotes) and tools for custom analysis of user-submitted sequences are provided.
57. Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
58. Karolchik, D. et al. Comparative genomic analysis using the UCSC genome browser. Methods Mol. Biol. 395, 17-34 (2007).
59. Prabhakar, S. et al. Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res. 16, 855-863 (2006).
60. Gregory, S.G. et al. A physical map of the mouse genome. Nature 418, 743-750 (2002).
61. Haas, B.J., Delcher, A.L., Wortman, J.R. & Salzberg, S.L. DAGchainer: A tool for mining segmental genome duplications and synteny. Bioinformatics 20, 3643-3646 (2004).
62. Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
63. Ohtsubo, Y., Ikeda-Ohtsubo, W., Nagata, Y. & Tsuda, M. GenomeMatcher: A graphical user interface for DNA sequence comparison. BMC Bioinformatics 9, 376 (2008).
64. Mouse Genome Sequencing Consortium. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
65. Galagan, J.E. et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438, 1105-1115 (2005).
66. Putnam, N.H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86-94 (2007).
67. Sinha, A.U. & Meller, J. Cinteny: Flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics 8, 82 (2007). a flexible web-based tool allowing investigators to view synteny at the level of whole genomes, individual pairs of chromosomes, or regions around markers of interest, which can be uploaded by the user.
68. Lewis, S.E. et al. Apollo: A sequence annotation editor. Genome Biol. 3, RESEARCH0082 (2002).
69. Dehal, P.S. & Boore, J.L. A phylogenomic gene cluster resource: The Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics 7, 201 (2006).
70. Krzywinski, M. et al. Circos: An information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).
71. Meyer, M., Munzner, T. & Pfister, H. MizBee: A multiscale synteny browser. IEEE Trans. Vis. Comput. Graph. 15, 897-904 (2009).
72. Miller, W. et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 17, 1797-1808 (2007).
73. Dubchak, I. Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools. Methods Mol. Biol. 395, 3-16 (2007).
74. Kent, W.J. et al. Evolution’s cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. USA 100, 11484-11489 (2003).
75. Brendel, V., Kurtz, S. & Pan, X. Visualization of syntenic relationships with SynBrowse. Methods Mol. Biol. 396, 153-163 (2007).
76. Carver, T. et al. Artemis and ACT: Viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24, 2672-2676 (2008).
77. Engels, R. et al. Combo: A whole genome comparative browser. Bioinformatics 22, 1782-1783 (2006).
78. Crabtree, J., Angiuoli, S.V., Wortman, J.R. & White, O.R. Sybil: Methods and software for multiple genome comparison and visualization. Methods Mol. Biol. 408, 93-108 (2007).
79. Wang, H., Su, Y., Mackey, A.J., Kraemer, E.T. & Kissinger, J.C. SynView: A GBrowse-compatible approach to visualizing comparative genome data. Bioinformatics 22, 2308-2309 (2006).
80. Shah, N. et al. Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments. Bioinformatics 20, 636-643 (2004).
81. Gottgens, B. et al. Long-range comparison of human and mouse SCL loci: Localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res. 11, 87-97 (2001).
82. Stothard, P. & Wishart, D.S. Circular genome visualization and exploration using CGView. Bioinformatics 21, 537-539 (2005).
83. Shannon, P.T., Reiss, D.J., Bonneau, R. & Baliga, N.S. The Gaggle: An open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics 7, 176 (2006).
84. Nicol, J.W., Helt, G.A., Blanchard, S.G. Jr., Raja, A. & Loraine, A.E. The Integrated Genome Browser: Free software for distribution and exploration of genome-scale data sets. Bioinformatics 25, 2730-2731 (2009).
85. Lyons, E. et al. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol. 148, 1772-1781 (2008).
86. Elnitski, L., Riemer, C., Burhans, R., Hardison, R. & Miller, W. MultiPipMaker: Comparative alignment server for multiple DNA sequences. Curr. Protoc. Bioinformatics Ch. 10, unit 10.14 (2005).
87. Mayor, C. et al. VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16, 1046-1047 (2000).
88. Youens-Clark, K., Faga, B., Yap, I.V., Stein, L. & Ware, D. CMap 1.01: A comparative mapping application for the Internet. Bioinformatics 25, 3040-3042 (2009).