Genewiz browser: An interactive tool for visualizing sequenced chromosomes

Standards in Genomic Sciences

Volumn 1, Issue 2, 2009, Pages 204-215

  Hallin, Peter F ^a   Stærfeldt, Hans Henrik ^a   Rotenberg, Eva ^a,b   Binnewies, Tim T ^a,c   Benham, Craig J ^d   Ussery, David W ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b Lersoe Parkalle 37 ^*  (Denmark)

^c Roche Diagnostics Ltd   (Switzerland)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROKARYOTA;

EID: 77957928699     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.28177     Document Type: Article

References (39)

1. Harrington ED, Singh AH, Doerks T, Letunic I, Von Mering C, Jensen LJ, Raes J, Bork P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci USA 2007; 104:13913-13918. PubMed doi:10.1073/pnas.0702636104
2. Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Staerfeldt HH, Rapacki K, Workman C et al. Prediction of human protein function from post-translational modifications and localization features. J Mol Biol 2002; 319:1257- 1265. PubMed doi:10.1016/S0022-2836(02)00379-0
3. Friedberg I. Automated protein function prediction the genomic challenge. Brief Bioinform 2006; 7:225. PubMed doi:10.1093/bib/bbl004
4. Jensen LJ, Friis C, Ussery DW. Three views of microbial genomes. Res Microbiol 1999; 150:773-777. PubMed doi:10.1016/S0923- 2508(99)00116-3
5. Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW. A DNA structural atlas for Escheri-chia coli. J Mol Biol 2000; 299:907-930. PubMed doi:10.1006/jmbi.2000.3787
6. Hall N. Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 2007; 210:1518-1525. PubMed doi:10.1242/jeb.001370
7. Holt RA, Jones SJ. The new paradigm of flow cell sequencing. Genome Res 2008; 18:839-846. PubMed doi:10.1101/gr.073262.107
8. Käller M, Lundeberg J, Ahmadian A. Arrayed identification of DNA signatures. Expert Rev Mol Diagn 2007; 7:65-76. PubMed doi:10.1586/14737159.7.1.65
9. Gupta PK. Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 2008; 26:602-611. PubMed doi:10.1016/j.tibtech.2008.07.003
10. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008; 26:1135-1145.PubMed doi:10.1038/nbt1486
11. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP et al. Rapid whole- genome mutational profiling using next- generation sequencing technologies. Genome Res 2008; 18:1638-1642. PubMed doi:10.1101/gr.077776.108
12. Lin F, Schröder H, Schmidt B. Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural Perspective. J VLSI Signal Process 2007; 48:185-188. doi:10.1007/s11265-007- 0088-z
13. Phillippy AM, Schatz MC, Pop M. Genome assembly forensics: finding the elusive misassembly. Genome Biol 2008; 9:R55. PubMed doi:10.1186/gb-2008-9-3-r55
14. Tolstrup N, Rouzé P, Brunak S. A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res 1997; 25:3159-3163. misctextPubMed/misctext doi:10.1093/nar/25.15.3159
15. Hallin PF, Binnewies TT, Ussery DW. The ge-nome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst 2008; 4:363-371. PubMed doi:10.1039/b717118h
16. Bolshoy A, McNamara P, Harrington RE, Trifonov EN. Curved DNA without A-A: experimental es- timation of all 16 DNA wedge angles. Proc Natl Acad Sci USA 1991; 88:2312-2316. PubMed doi:10.1073/pnas.88.6.2312
17. Brukner I, Sánchez R, Suck D, Pongor S. Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleo- tides. EMBO J 1995; 14:1812-1818. misctextPubMed/misctext
18. van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR. Strand misalignments lead to quasipalindrome correction. Trends Genet 2003; 19:365-369. PubMed doi:10.1016/S0168-9525(03)00136-7
19. Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 1998; 95:11163-11168. PubMed doi:10.1073/pnas.95.19.11163
20. Ornstein RL, Rein R, Breen DL, MacElroy RD. An optimized potential function for the calculation of nucleic acid interaction energies. I- Base stacking. Biopolymers 1978; 17:2341-2360. doi:10.1002/bip.1978.360171005
21. Satchwell SC, Drew HR, Travers AA. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 1986; 191:659-675. PubMed doi:10.1016/0022-2836(86)90452-3
22. Ussery D, Soumpasis DM, Brunak S, Staerfeldt HH, Worning P, Krogh A. Bias of purine stretches in sequenced chromosomes. Comput Chem 2002; 26:531-541. PubMed doi:10.1016/S0097- 8485(02)00013-X
23. Wang H, Benham CJ. Superhelical destabilization in regulatory regions of stress response genes. PLOS Comput Biol 2008; 4:e17. PubMed doi:10.1371/journal.pcbi.0040017
24. Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M. Pseudogene.org: a comprehensive database and compar- ison platform for pseudogene annotation. Nucleic Acids Res 2007; 35:D55-D60. PubMed doi:10.1093/nar/gkl851
25. Hallin PF, Ussery DW. CBS Genome Atlas Data- base: a dynamic storage for bioinformatic results and sequence data. Bioinformatics 2004; 20:3682-3686. PubMed doi:10.1093/bioinformatics/bth423
26. Blattner FR, Plunkett G, Bloch CA, Perna NT,Burland V, Riley M, Collado-Vides J, Glasner JD,Rode CK, Mayhew GF et al. The complete ge- nome sequence of Escherichia coli K-12. Science 1997; 277:1453-1462. PubMed doi:10.1126/science.277.5331.1453
27. Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, Chillingworth T, Davies RM, Feltwell T, Holroyd S et al. The genome se- quence of the food-borne pathogen Campylobac- ter jejuni reveals hypervariable sequences. Nature 2000; 403:665-668. PubMed doi:10.1038/35001088
28. Deng W, Liou SR, Plunkett G, Mayhew GF, Rose DJ, Burland V, Kodoyianni V, Schwartz DC,Blattner FR. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol 2003; 185:2330-2337. misctextPubMed doi:10.1128/JB.185.7.2330-2337.2003/misctext
29. Brett PJ, DeShazer D, Woods DE. Burkholderia thailandensis sp. nov., a Burkholderia pseudomal-lei-like species. Int J Syst Bacteriol 1998; 48:317-320. PubMed
30. Smith MD, Angus BJ, Wuthiekanun V, White NJ.Arabinose assimilation defines a nonvirulent bio-type of Burkholderia pseudomallei. Infect Immun 1997; 65:4319-4321. PubMed
31. Ong C, Ooi CH, Wang D, Chong H, Ng KC, Ro-drigues F, Lee MA, Tan P. Patterns of large-scale Hallin, et al.genomic variation in virulent and avirulent Burk- holderia species. Genome Res 2004; 14:2295-2307. PubMed doi:10.1101/gr.1608904
32. Hirvonen CA, Ross W, Wozniak CE, Marasco E, Anthony JR, Aiyar SE, Newburn VH, Gourse RL. Contributions of UP elements and the transcrip- tion factor FIS to expression from the seven rrn P1 promoters in Escherichia coli. J Bacteriol 2001; 183:6305-6314. PubMed doi:10.1128/JB.183.21.6305-6314.2001
33. Ross W, Salomon J, Holmes WM, Gourse RL.Activation of Escherichia coli leuV transcription by FIS. J Bacteriol 1999; 181:3864-3868. PubMed
34. Wang H, Noordewier M, Benham CJ. Stress- induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely asso- ciated with promoters. Genome Res 2004; 14:1575-1584. PubMed doi:10.1101/gr.2080004
35. Bauer BF, Kar EG, Elford RM, Holmes WM. Sequence determinants for promoter strength in the leuV operon of Escherichia coli. Gene 1988; 63:123-134. PubMed doi:10.1016/0378- 1119(88)90551-3
36. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009; 25:119-120. PubMed doi:10.1093/bioinformatics/btn578
37. Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M. Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics 2009; 10:31. PubMed doi:10.1186/1471-2105-10-31
38. Pritchard L, White JA, Birch PR, Toth IK. Geno- meDiagram: a python package for the visualiza-tion of large-scale genomic data. Bioinformatics 2006; 22:616-617. PubMed doi:10.1093/bioinformatics/btk021
39. Krzywinski M, Schein J, Birol I, Connors J, Gas- coyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genom- ics. Genome Res 2009; 19:1639-1645. PubMed doi:10.1101/gr.092759.109