GenomeView examples: Difference between revisions

From CoGepedia
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 32: Line 32:
===rRNA genes===
===rRNA genes===
[[Image:GenomeView-rRNA.png|thumb|800px|center|Microbial (archaea) genomic region with 23S and 16S rRNA genes drawn as wide gray arrows]]
[[Image:GenomeView-rRNA.png|thumb|800px|center|Microbial (archaea) genomic region with 23S and 16S rRNA genes drawn as wide gray arrows]]
----


===Pseudogenes===
===Pseudogenes===
[[Image:GenomeView-pseudogene-2.png|thumb|800px|center|Microbial (archaea) genomic region with many pseudogenes drawn as orange-red arrows]]
[[Image:GenomeView-pseudogene-2.png|thumb|800px|center|Microbial (archaea) genomic region with many pseudogenes drawn as orange-red arrows]]
----


===Wobble GC content filter===
===Wobble GC content filter===
Line 40: Line 42:
[[Image:GenomeView-wobbleGC2.png|thumb|800px|center|Wobble GC content colored for Chlamydomonas reinhardtii chloroplast genome.  Red means low GC content in codon wobble positions]]
[[Image:GenomeView-wobbleGC2.png|thumb|800px|center|Wobble GC content colored for Chlamydomonas reinhardtii chloroplast genome.  Red means low GC content in codon wobble positions]]
[[Image:GenomeView-wobbleGC3.png|thumb|800px|center|Wobble GC content colored for Chlamydomonas reinhardtii mitochondria genome.  Yellow means ~50% GC content in codon wobble positions]]
[[Image:GenomeView-wobbleGC3.png|thumb|800px|center|Wobble GC content colored for Chlamydomonas reinhardtii mitochondria genome.  Yellow means ~50% GC content in codon wobble positions]]
----


===GEvo Links===
===GEvo Links===
[[Image:GenomeView GEvo-links.png|thumb|800px|center|GenomeView showing glyphs for links to GEvo. These glyphs are blue "links" and are displayed when a genomic feature has a link to GEvo for syntenic analysis of syntelogs.]]
[[Image:GenomeView GEvo-links.png|thumb|800px|center|GenomeView showing glyphs for links to GEvo. These glyphs are blue "links" and are displayed when a genomic feature has a link to GEvo for syntenic analysis of syntelogs.]]
----


===Repeat Regions===
===Repeat Regions===
[[Image:GenomeView-Repeat-regions.png|thumb|800px|center|GenomeView showing repeat regions as black and blue boxes around a sequence and gene. There are two IS elements highlighted by these boxes that have each jumped into a gene and disrupted it.]]
[[Image:GenomeView-Repeat-regions.png|thumb|800px|center|GenomeView showing repeat regions as black and blue boxes around a sequence and gene. There are two IS elements highlighted by these boxes that have each jumped into a gene and disrupted it.]]
----


===Other Features===
===Other Features===
[[Image:GenomeView-Other-Feature-Phage.png|thumb|800px|center|GenomeView showing "other features" as orange boxes. This other features is a prophage that has integrated in the genome of Escherichia coli K12 strain K-12 substrain MG1655.]]
[[Image:GenomeView-Other-Feature-Phage.png|thumb|800px|center|GenomeView showing "other features" as orange boxes. This other features is a prophage that has integrated in the genome of Escherichia coli K12 strain K-12 substrain MG1655.]]
----

Revision as of 04:04, 21 February 2010

CoGe's genome visualization library, GeLo, is very flexible in the types of graphics it can produce. The best way to figure out what something means in an image from CoGe is to scroll through this list of images, find something that looks similar, and then read the description.

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

Chromosome 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

rRNA genes

Microbial (archaea) genomic region with 23S and 16S rRNA genes drawn as wide gray arrows

Pseudogenes

Microbial (archaea) genomic region with many pseudogenes drawn as orange-red arrows

Wobble GC content filter

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

GEvo Links

GenomeView showing glyphs for links to GEvo. These glyphs are blue "links" and are displayed when a genomic feature has a link to GEvo for syntenic analysis of syntelogs.

Repeat Regions

GenomeView showing repeat regions as black and blue boxes around a sequence and gene. There are two IS elements highlighted by these boxes that have each jumped into a gene and disrupted it.

Other Features

GenomeView showing "other features" as orange boxes. This other features is a prophage that has integrated in the genome of Escherichia coli K12 strain K-12 substrain MG1655.
Retrieved from "https://genomevolution.org/wiki/index.php?title=GenomeView_examples&oldid=1750"