File:TABASCO-A-single-molecule-base-pair-resolved-gene-expression-simulator-1471-2105-8-480-S1.ogv
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[edit]DescriptionTABASCO-A-single-molecule-base-pair-resolved-gene-expression-simulator-1471-2105-8-480-S1.ogv |
English: Additional File 1 Visualization of T7 genome simulation using Tabasco. We developed a general visualization tool for depicting graphically and dynamically depicting output from Tabasco. Here, we show output from a Tabasco simulation of three T7 phage simultaneously infecting a single cell over the course of 25 minutes. Each of the three white lines at the top represents a distinct copy of the 39,937 bp T7 genome. The T7 and E. coli RNA polymerases are shown as blue and yellow lines moving directly along and above the genomes; directly below the genomes are promoters (dark blue) and terminators (dark red). In addition, the extent of each genomes entry is shown as a solid white line that extends above and below the genome representation (while genome entry is occurring). Protein levels (solid bars) and mRNA levels (white lines) of T7 genes and other host RNA polymerase and ribosome levels are plotted as numbers of molecules per cell on a log-scale below the genome depictions. Each frame is a snapshot of the simulation taken at 5-second intervals; time is displayed in seconds directly below the genome representations. |
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Source | Kosuri S, Kelly J, Endy D (2007). "TABASCO: A single molecule, base-pair resolved gene expression simulator". BMC Bioinformatics. DOI:10.1186/1471-2105-8-480. PMID 18093293. PMC: 2242808. | ||
Author | Kosuri S, Kelly J, Endy D | ||
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This file is licensed under the Creative Commons Attribution 2.0 Generic license.
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current | 02:10, 21 November 2012 | 30 s, 1,024 × 768 (6.24 MB) | Open Access Media Importer Bot (talk | contribs) | Automatically uploaded media file from Open Access source. Please report problems or suggestions here. |
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Short title | Additional File 1 |
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Author | Kosuri S, Kelly J, Endy D |
Usage terms | http://creativecommons.org/licenses/by/2.0/ |
Image title | Visualization of T7 genome simulation using Tabasco. We developed a general visualization tool for depicting graphically and dynamically depicting output from Tabasco. Here, we show output from a Tabasco simulation of three T7 phage simultaneously infecting a single cell over the course of 25 minutes. Each of the three white lines at the top represents a distinct copy of the 39,937 bp T7 genome. The T7 and E. coli RNA polymerases are shown as blue and yellow lines moving directly along and above the genomes; directly below the genomes are promoters (dark blue) and terminators (dark red). In addition, the extent of each genomes entry is shown as a solid white line that extends above and below the genome representation (while genome entry is occurring). Protein levels (solid bars) and mRNA levels (white lines) of T7 genes and other host RNA polymerase and ribosome levels are plotted as numbers of molecules per cell on a log-scale below the genome depictions. Each frame is a snapshot of the simulation taken at 5-second intervals; time is displayed in seconds directly below the genome representations. |
Software used | Xiph.Org libtheora 1.1 20090822 (Thusnelda) |
Date and time of digitizing | 2007 |
Categories:
- Bacteriophage T7
- Base pairing
- Binding sites
- Computer simulations
- DNA-directed RNA polymerases
- Videos of Escherichia coli
- Gene expression
- Gene expression profiling
- Gene expression regulation
- Fungal genome
- Knowledge bases
- Videos of statistics
- Transcriptional regulatory elements
- DNA sequence analysis
- Software design
- Videos of transcription factors
- Videos of viral proteins