Main public logs

Combined display of all available logs of CoGepedia. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 18:12, 16 September 2009 Elyons talk contribs uploaded File:CoGe-Front-End.png (CoGe's web-tools have several applications for initiating an analysis. OrganismView: Search for an organism by name or description CoGeBlast: Blast a sequence against any number of genomes FeatView: Search for a genomic feature (e.g. gene) by name SynM)
• 17:56, 16 September 2009 Elyons talk contribs uploaded File:K12-HGT.png (A cryptic prophage is easily visualized in the genome of Escherichia coli K12 substrain MG1655 by adding the visualization layer for coloring coding sequence by the percent GC in their wobble positions. While the majority of coding sequence in K12 have a)
• 17:05, 30 August 2009 Elyons talk contribs uploaded a new version of File:SynPlot-Chr1-At-v-Al.png ((Syntenic dotplot and synonymous substitution histogram of Chromosome 1 of Arabidopsis thaliana and Arabidopsis lyrata. Syntenic gene pairs were identified by DAGChainer, and colored based on their synonymous substitution rate as calculated by CodeML. S))
• 17:00, 30 August 2009 Elyons talk contribs uploaded a new version of File:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.hist-1.png ((Histogram of synonymous rate change data for syntenic gene pairs between Arabidopsis thaliana and Arabidopsis lyrata. Results can be regenerated here: http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=3068;dsgid2=8;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;d)
• 16:59, 30 August 2009 Elyons talk contribs uploaded a new version of File:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.png ((Syntenic dotplot of Arabidopsis thaliana versus Arabidopsis lyrata. Syntenic gene pairs identified by DagChainer have been colored based on there synonymous rate (kS) data as calculated by CODEML. Results can be regenerated at http://synteny.cnr.berkeley)
• 21:57, 28 August 2009 Elyons talk contribs uploaded File:GEvo-At-Al.png (GEvo analysis of syntenic regions from Arabidopsis thaliana and Arabidopsis lyrata. At1-Al1 and At2-At2 are derived from the speciation of the taxa. This is evidenced by the strong spatial syntenic signal as seen by the extensive collinear arrangement o)
• 16:46, 28 August 2009 Elyons talk contribs uploaded File:SynPlot-Chr1-At-v-Al.png (Syntenic dotplot and synonymous substitution histogram of Chromosome 1 of Arabidopsis thaliana and Arabidopsis lyrata. Syntenic gene pairs were identified by DAGChainer, and colored based on their synonymous substitution rate as calculated by CodeML. S)
• 18:36, 27 August 2009 Elyons talk contribs uploaded File:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.hist-1.png (Histogram of synonymous rate change data for syntenic gene pairs between Arabidopsis thaliana and Arabidopsis lyrata. Results can be regenerated here: http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=3068;dsgid2=8;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;d)
• 18:29, 27 August 2009 Elyons talk contribs uploaded a new version of File:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.png (Syntenic dotplot of Arabidopsis thaliana versus Arabidopsis lyrata. Syntenic gene pairs identified by DagChainer have been colored based on there synonymous rate (kS) data as calculated by CODEML. Results can be regenerated at http://synteny.cnr.berkeley)
• 00:46, 26 August 2009 Elyons talk contribs uploaded a new version of File:GEvo-4-at-cp-vv.png (Syntenic comparison of 4 regions of Arabidopsis thaliana to one region each of Carica papaya and Vitis vinifera. Since these lineages diverged, Arabidopsis has had two sequential whole genome duplication events while papaya and grape have had none. This l)
• 00:45, 26 August 2009 Elyons talk contribs deleted page File:GEvo-4-at-cp-vv2.png
• 00:44, 26 August 2009 Elyons talk contribs uploaded File:GEvo-4-at-cp-vv2.png
• 23:14, 25 August 2009 Elyons talk contribs uploaded File:Genome-phylogeny-At-Cp-Vv.png (Since their divergence, the Arabidopsis lineage has undergone two sequential whole genome duplication events while papaya and grape have had none. This means that for each genomic region of grape, there is one corresponding syntenic region in papaya, and)
• 23:10, 25 August 2009 Elyons talk contribs uploaded File:GEvo-4-at-cp-vv.png (Syntenic comparison of 4 regions of Arabidopsis thaliana to one region each of Carica papaya and Vitis vinifera. Since these lineages diverged, Arabidopsis has had two sequential whole genome duplication events while papaya and grape have had none. Thi)
• 23:19, 18 August 2009 Elyons talk contribs uploaded File:GEvo-setup.png (GEvo's sequence submission setup)
• 22:55, 18 August 2009 Elyons talk contribs uploaded File:Gobe-interface.png (Image showing GEvo results in Gobe interface)
• 21:38, 12 August 2009 Elyons talk contribs uploaded File:GenomeView-get feats.png (GenomeView. How to extract features from a genomic view.)
• 21:33, 12 August 2009 Elyons talk contribs uploaded File:GenomeView-get seq.png (GenomeView with how to get genomic sequence annotated)
• 21:18, 12 August 2009 Elyons talk contribs uploaded File:GenomeView-information.png (GenomeView's popup information)
• 20:54, 12 August 2009 Elyons talk contribs uploaded File:GenomeView-navigation.png (GenomeView with navigation buttons annotated.)
• 18:13, 11 August 2009 Elyons talk contribs uploaded File:GenomeView.png (GenomeView.)
• 18:05, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-masked.png (GenomeView showing masked genomic regions as purple from the genome of Zea Mays.)
• 18:01, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-Unsequenced.png (GenomeView with show unsequenced genomic regions as orange from the genome of Carica papaya.)
• 17:55, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-wobbleGC3.png (GenomeView with CDS wobble GC content colored yellow for ~50% GC content in codon wobble positions. Chlamydomonas reinhardtii mitochondria genome. )
• 17:55, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-wobbleGC2.png (GenomeView with CDS wobble GC content colored red for low GC content in codon wobble positions. Chlamydomonas reinhardtii chloroplast genome. )
• 17:54, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-wobbleGC1.png (GenomeView with CDS wobble GC content colored green for high GC content in codon wobble positions. Chlamydomonas reinhardtii genome.)
• 17:46, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-pseudogene-2.png (GenomeView showing many neighboring pseudogenes (orange-red) in the genome of Sulfolobus islandicus strain L.S.2.15. )
• 17:45, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-pseudogene.png (GenomeView pseudo gene (orange-red) in the genome of Sulfolobus islandicus strain L.S.2.15. )
• 17:45, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-rRNA.png (GenomeView showing 23S and 16S rRNA genes in the genome of Sulfolobus islandicus strain L.S.2.15. Note the difference in GC conetent of rRNA genes as determined by background color being greener than surround regions.)
• 17:36, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-CDS.png (GenomeView showing background GC, gene, mRNA, and CDS models. From Arabidopsis genome.)
• 17:36, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-mRNA.png (GenomeView showing background GC, gene, and mRNA models. From Arabidopsis genome.)
• 17:34, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-gene.png (GenomeView showing background GC and gene models. From Arabidopsis genome.)
• 17:32, 11 August 2009 Elyons talk contribs uploaded File:GenomeView-background.png (GenomeView showing AT/GC content)
• 19:01, 10 August 2009 Elyons talk contribs uploaded File:GEvo-local-dup-show-overlap.png (GEvo results with "auto adjust" HSP and Genomic Features turned on. This causes GEvo to find genomic features and blast-hits that overlap at the same position, and drawn them such that they are separated in order to identify local duplications in a genom)
• 18:46, 10 August 2009 Elyons talk contribs uploaded File:GEvo-local-dup-no-show-overlap.png (Example of GEvo result with local duplications that are obfuscated by not showing separating overlapping HSPs. Comparison is between orthologous regions of Arabidopsis thaliana and Arabidopsis lyrata. (A) No wedges drawn connecting regions of sequence s)
• 18:33, 10 August 2009 Elyons talk contribs uploaded File:GEvo-show-overlapping.png (GEvo's options for showing overlapping genomic features and HSPs.)
• 18:07, 10 August 2009 Elyons talk contribs deleted page CoGeBlast Documentation (mergin this page with CoGeBlast page. No reason for separate pages)
• 20:01, 7 August 2009 Elyons talk contribs uploaded File:GEvo-with-labels.png (Example GEvo result with contigs, hsp labels, and genomic feature labels drawn.)
• 20:00, 7 August 2009 Elyons talk contribs uploaded File:GEvo-contigs-and-labels.png (Shows where the options are for drawing labels and contigs for GEvo results.)
• 00:32, 7 August 2009 Elyons talk contribs uploaded File:GeLo-example.png (Example of GeLo's graphics with different genomic "stuff" labeled.)
• 00:22, 7 August 2009 Elyons talk contribs uploaded File:Diploidization-cartoon.png (Cartoon of the process of diploidization following a whole genome duplication event. While the overall gene content is reduced to one that is similar to the pre-duplicated ancestory, the overall architecture of the genome will be vastly different due to )
• 00:17, 7 August 2009 Elyons talk contribs uploaded File:Fractionation-cartoon.png (Cartoon of fractionation following a genome duplication event. Colored circle represent genes along a genomic region. Following a genome duplication, all genomic content including chromosomes and their underlying gene content is contemporaneously copied)
• 23:30, 4 August 2009 Elyons talk contribs uploaded File:At-Cp-Retention.png
• 23:21, 4 August 2009 Elyons talk contribs uploaded File:At-Cp-Fractionation.png (Example GEvo analysis of fraction of gene content between 4 syntenic regions of Arabidopsis thaliana and one syntenic region of Carica papaya. Since their divergence, Arabidopsis thaliana has had two whole genome duplication events while papaya has had n)
• 18:08, 4 August 2009 Elyons talk contribs uploaded File:GEvo-links.png (Screen-shot of the results of a GEvo analysis with links for regenerating and saving the analysis labeled.)
• 21:22, 14 July 2009 Elyons talk contribs uploaded File:Crab spider.jpg (Yellow Crab spider )
• 21:20, 14 July 2009 Elyons talk contribs uploaded File:100px-Nsf1.jpg (NSF logo)
• 05:30, 13 May 2009 Elyons talk contribs uploaded File:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.hist.png (Histogram of Ks values for the image master_3068_8.CDS-CDS.blastn_geneorder_D20_g10_A5.w2000.ks.png)
• 05:06, 13 May 2009 Elyons talk contribs uploaded File:Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.png (Syntenic dotplot between Arabidopsis thaliana and Arabidopsis lyrata. Regions of synteny were identified by DAGchainer. Syntelogs are colored based on their relative synonymous mutation rate as determined by CODEML. )
• 04:47, 13 May 2009 Elyons talk contribs uploaded File:Grape-tomato-synteny.png (250kb region of tomato aligned with a 500kb region of grape. Regenerated at http://tinyurl.com/qjpcvv)