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).

• 19:26, 29 December 2009 Elyons talk contribs uploaded File:CoGe genomes database.png (CoGe's genomes database schema.)
• 22:30, 28 December 2009 Elyons talk contribs uploaded File:DH10B-WG3110-Inversion.png (GEvo analysis of the inversion break-points between E. coli DH10B and W3110. At the inversion breakpoint in all regions is a ribosomal gene cassette. http://tinyurl.com/yatxhkt)
• 21:15, 28 December 2009 Elyons talk contribs uploaded File:Master 4241 4243.CDS-CDS.blastn geneorder D20 g10 A5.w500.png (Syntenic dotplot between Escherichia coli K12 substrains DH10B and W3110 showning an inversion. http://tinyurl.com/ya4glwm)
• 19:57, 28 December 2009 Elyons talk contribs uploaded File:K12-DH10B-codon-usage.png (Codon usage table for Eschericia coli K12 DH10B. Generating by OrganismView: http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?oid=24289)
• 19:33, 28 December 2009 Elyons talk contribs uploaded a new version of File:Gevo-synteny.png (Intra-genomic synteny from the genome of Arabidopsis thaliana. http://tinyurl.com/noul6b)
• 19:32, 28 December 2009 Elyons talk contribs uploaded a new version of File:Gevo-synteny.png (Comparison of two syntenic genomic regions from the genome of Arabidopsis thaliana. Its genome, as with all angiosperm genomes, has undergone ancient whole genome duplication events. This image shows a collinear arrangement of genes which is evidence th)
• 01:56, 23 December 2009 Elyons talk contribs uploaded File:Zm-Sb-6way.png (Comparison of syntenic regions from maize and sorghum, dating back to the pre-grass whole genome duplication event. This event has 6 panels, 4 from maize and 2 from sorghum. http://tinyurl.com/ycszpqs)
• 01:00, 23 December 2009 Elyons talk contribs uploaded File:Maize-sorghum-genome-history.png (Cartoon of the genome history of maize and sorghum. Prior to their divergence is a whole genome duplication event that is also shared among all the grasses. After their divergence, maize underwent one whole genome duplication event.)
• 00:50, 23 December 2009 Elyons talk contribs uploaded File:Master 6807 8082.CDS-CDS.blastn geneorder D40 g20 A10.w1200.gene.ks.png (Syntenic dotplot with Ks coloration of maize versus sorghum. Genes are used for axis metrics. Results can be regenerated at: http://tinyurl.com/y9e778s)
• 23:10, 15 October 2009 Elyons talk contribs uploaded File:GEvo-image-parameters-hsp-limit.png (Setting HSP limits in GEvo)
• 23:08, 15 October 2009 Elyons talk contribs uploaded File:GEvo-ra2-cns-discovery.png (Using blastn in GEvo to identify conserved noncoding sequences for ramora2 in grasses)
• 23:07, 15 October 2009 Elyons talk contribs uploaded File:GEvo-blastn.png (Selecting blastn in GEvo)
• 23:06, 15 October 2009 Elyons talk contribs uploaded File:GEvo-identifying-conserved-sequence-ra2.png (Identifying conserved sequence around ramora2 in GEvo)
• 23:04, 15 October 2009 Elyons talk contribs uploaded File:GEvo-change-region-extent.png (Changing the amount of up and downstream sequence for a sequence submission in GEvo)
• 23:02, 15 October 2009 Elyons talk contribs uploaded File:GEvo-add-to-all.png (Option increase up and downstream sequence to all sequence submissions)
• 23:01, 15 October 2009 Elyons talk contribs uploaded File:GEvo-sequence-needs-rc.png (Identifying a sequence that needs to be reverse complemented in GEvo)
• 23:00, 15 October 2009 Elyons talk contribs uploaded File:GEvo-reverse-complement-option.png (Selecting the reverse complement option for a sequence submission in GEvo)
• 22:58, 15 October 2009 Elyons talk contribs uploaded File:GEvo-direct-submission-check.png (Checking a direct sequence submission in GEvo)
• 22:46, 15 October 2009 Elyons talk contribs uploaded File:Ra2-GEvo-result.png (GEvo result of ra2 in syntenic region between Brachypodium and Rice)
• 22:44, 15 October 2009 Elyons talk contribs uploaded File:GEvo-manual-add-sequence.png (Manually adding a sequence to a GEvo analysis by pasting in a sequence into the sequence submission box.)
• 22:43, 15 October 2009 Elyons talk contribs uploaded File:CoGeBlast-HSPTable.png (HSP table from CoGeBlast)
• 22:41, 15 October 2009 Elyons talk contribs uploaded File:Ra2-CoGeBlast.png (Configuring CoGeBlast to search multiple grass genomes.)
• 22:39, 15 October 2009 Elyons talk contribs uploaded File:NM 001138446.png (Screen-shot of NM_001138446 from NCBI)
• 01:26, 15 October 2009 Elyons talk contribs uploaded File:Master 6871 4242.genomic-CDS.blastn geneorder D100 g50 A5.w2000.ass.png (Syntenic comparison of a de novo assembled E. coli genome to a reference genome using SynMap and SynMap's algorithm to order contigs by their best syntenic path.)
• 01:22, 15 October 2009 Elyons talk contribs uploaded File:Master 6871 4242.genomic-CDS.blastn geneorder D100 g50 A5.w2000.png (Comparison of a de novo assembled E. coli genome sequenced using the whole genome shotgun approached without any bac-ends to order contigs.)
• 23:04, 23 September 2009 Elyons talk contribs uploaded File:OrganismView Example Search.png (Example screen-shot from OrganismView when searching for any organism's whose name contains "arabid".)
• 22:34, 23 September 2009 Elyons talk contribs uploaded File:OrganismView home.png (Initial page for OrganismView)
• 22:43, 21 September 2009 Elyons talk contribs uploaded File:K12-MG1655-DH10B-syn dotplot.png (Syntenic dotplot between two Escherichia coli K12 strains. DH10B is on x-axis. MG1655 is on the y-axis. Results can be regenerated at: http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=4241;dsgid2=4242;D=20;g=5;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder)
• 18:17, 16 September 2009 Elyons talk contribs uploaded File:CoGe-Analysis-Network.png (CoGe has several interconnected web-tools. Since each tool performs a specific task (e.g. displaying a list of features, viewing a fasta sequence), tools are linked together to allow researches the ability to move through their analyses in a variety of w)
• 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.)