GenomeView examples: Difference between revisions

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===Overview===
===Overview===
[[Image:GeLo-example.png|thumb|800px|left|Overview of [[GenomeView]]'s visualization using the [[GeLo]] genomic visualization library.  Background of chromosome is colored green for GC rich regions and while for AT rich regions.  Gene models are drawn as composite colored arrows such that gray is the extent of the gene, blue is mRNA, and green is protein coding [[CDS]] sequence. Overlapping genomic features are detected and expanded to show alternatively spiced transcripts]]
[[Image:GeLo-example.png|thumb|800px|Overview of [[GenomeView]]'s visualization using the [[GeLo]] genomic visualization library.  Background of chromosome is colored green for GC rich regions and while for AT rich regions.  Gene models are drawn as composite colored arrows such that gray is the extent of the gene, blue is mRNA, and green is protein coding [[CDS]] sequence. Overlapping genomic features are detected and expanded to show alternatively spiced transcripts]]


===Background===
===Background===
[[Image:GenomeView-background.png|thumb|800px|left|Background of chromosome colored green to show GC rich regions and white to show AT rich regions]]
[[Image:GenomeView-background.png|thumb|800px|Background of chromosome colored green to show GC rich regions and white to show AT rich regions]]
[[Image:GeLo-nucleotides.png|thumb|left|800px|Example GeLo graphics using images of nucleotides in the background.  These are also colored green for GC and white for AT]]
[[Image:GeLo-nucleotides.png|thumb|left|800px|Example GeLo graphics using images of nucleotides in the background.  These are also colored green for GC and white for AT]]


===Genes===
===Genes===
[[Image:GenomeView-gene.png|thumb|800px|left|Gene models drawn as gray arrows]]
[[Image:GenomeView-gene.png|thumb|800px|Gene models drawn as gray arrows]]


===mRNAs===
===mRNAs===
[[Image:GenomeView-mRNA.png|thumb|800px|left|mRNA drawn as blue arrows (on top of gray genes)]]
[[Image:GenomeView-mRNA.png|thumb|800px|mRNA drawn as blue arrows (on top of gray genes)]]
[[Image:GenomeView-CDS.png|thumb|800px|left|Protein coding regions (CDS) drawn as green arrows (on top of gray genes and blue mRNAs)]]
 
[[Image:GenomeView-Unsequenced.png|thumb|800px|left|Genomic region with unsequenced regions colored orange from the genome of Carica papaya]]
===CDSs===
[[Image:GenomeView-CDS.png|thumb|800px|Protein coding regions (CDS) drawn as green arrows (on top of gray genes and blue mRNAs)]]
 
===Unsequenced regions===
[[Image:GenomeView-Unsequenced.png|thumb|800px|Genomic region with unsequenced regions colored orange from the genome of Carica papaya]]
 
===Masked regions===
[[Image:GenomeView-masked.png|thumb|800px|left|Genomic region with masked sequence colored purple]]
[[Image:GenomeView-masked.png|thumb|800px|left|Genomic region with masked sequence colored purple]]
[[Image:GenomeView-rRNA.png|thumb|800px|left|Microbial (archaea) genomic region with 23S and 16S rRNA genes drawn as wide gray arrows]]
[[Image:GenomeView-rRNA.png|thumb|800px|left|Microbial (archaea) genomic region with 23S and 16S rRNA genes drawn as wide gray arrows]]

Revision as of 19:29, 5 February 2010

Overview

Overview of GenomeView's visualization using the GeLo genomic visualization library. Background of chromosome is colored green for GC rich regions and while for AT rich regions. Gene models are drawn as composite colored arrows such that gray is the extent of the gene, blue is mRNA, and green is protein coding CDS sequence. Overlapping genomic features are detected and expanded to show alternatively spiced transcripts

Background

Background of chromosome colored green to show GC rich regions and white to show AT rich regions
Example GeLo graphics using images of nucleotides in the background. These are also colored green for GC and white for AT

Genes

Gene models drawn as gray arrows

mRNAs

mRNA drawn as blue arrows (on top of gray genes)

CDSs

Protein coding regions (CDS) drawn as green arrows (on top of gray genes and blue mRNAs)

Unsequenced regions

Genomic region with unsequenced regions colored orange from the genome of Carica papaya

Masked regions

Genomic region with masked sequence colored purple
Microbial (archaea) genomic region with 23S and 16S rRNA genes drawn as wide gray arrows
Microbial (archaea) genomic region with many pseudogenes drawn as orange-red arrows
Wobble GC content colored for Chlamydomonas reinhardtii genome. Green means high GC content in codon wobble positions
Wobble GC content colored for Chlamydomonas reinhardtii chloroplast genome. Red means low GC content in codon wobble positions
Wobble GC content colored for Chlamydomonas reinhardtii mitochondria genome. Yellow means ~50% GC content in codon wobble positions
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