Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data

被引：86

作者：

Baerends, RJS ^{[1
]}

Smits, WK ^{[1
]}

de Jong, A ^{[1
]}

Hameon, LW ^{[1
]}

Kok, J ^{[1
]}

Kuipers, OP ^{[1
]}

机构：

[1] Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, NL-9751 NN Haren, Netherlands

来源：

GENOME BIOLOGY | 2004年 / 5卷 / 05期

关键词：

D O I：

10.1186/gb-2004-5-5-r37

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Genome2D is a Windows-based software tool for visualization of bacterial transcriptome and customized datasets on linear chromosome maps constructed from annotated genome sequences. Genome2D facilitates the analysis of transcriptome data by using different color ranges to depict differences in gene-expression levels on a genome map. Such output format enables visual inspection of the transcriptome data, and will quickly reveal transcriptional units, without prior knowledge of expression level cutoff values. The compiled version of Genome2D is freely available for academic or non-profit use from http://molgen.biol.rug.nl/molgen/research/molgensoftware.php.

引用

页数：6

共 46 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL
ALTSCHUL, SF
GISH, W
MILLER, W
MYERS, EW
LIPMAN, DJ
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) : 403 - 410
[2] Bailey T L, 1995, Proc Int Conf Intell Syst Mol Biol, V3, P21
[3] Microarray analysis of the Bacillus subtilis K-state:: genome-wide expression changes dependent on ComK
Berka, RM
Hahn, J
Albano, M
Draskovic, I
Persuh, M
Cui, XJ
Sloma, A
Widner, W
Dubnau, D
[J]. MOLECULAR MICROBIOLOGY, 2002, 43 (05) : 1331 - 1345
[4] The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp lactis IL1403
Bolotin, A
Wincker, P
Mauger, S
Jaillon, O
Malarme, K
Weissenbach, J
Ehrlich, SD
Sorokin, A
[J]. GENOME RESEARCH, 2001, 11 (05) : 731 - 753
[5] A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli
Bulyk, ML
McGuire, AM
Masuda, N
Church, GM
[J]. GENOME RESEARCH, 2004, 14 (02) : 201 - 208
[6] Bulyk ML, 2004, GENOME BIOL, V5
[7] Regulatory element detection using correlation with expression
Bussemaker, HJ
Li, H
Siggia, ED
[J]. NATURE GENETICS, 2001, 27 (02) : 167 - 171
[8] Microarray expression profiling: capturing a genome-wide portrait of the transcriptome
Conway, T
Schoolnik, GK
[J]. MOLECULAR MICROBIOLOGY, 2003, 47 (04) : 879 - 889
[9] Exploring the metabolic and genetic control of gene expression on a genomic scale
DeRisi, JL
Iyer, VR
Brown, PO
[J]. SCIENCE, 1997, 278 (5338) : 680 - 686
[10] Biodiversity: Microbial genomes multiply
Doolittle, RF
[J]. NATURE, 2002, 416 (6882) : 697 - 700

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