Upload log
Below is a list of the most recent file uploads. See the gallery of new files for a more visual overview.
(newest | oldest) View (newer 50 | older 50) (20 | 50 | 100 | 250 | 500)- 16:44, 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.)
- 16:43, 15 October 2009 Elyons (Talk | contribs) uploaded File:CoGeBlast-HSPTable.png (HSP table from CoGeBlast)
- 16:41, 15 October 2009 Elyons (Talk | contribs) uploaded File:Ra2-CoGeBlast.png (Configuring CoGeBlast to search multiple grass genomes.)
- 16:39, 15 October 2009 Elyons (Talk | contribs) uploaded File:NM 001138446.png (Screen-shot of NM_001138446 from NCBI)
- 19:26, 14 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.)
- 19:22, 14 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.)
- 17:42, 5 October 2009 Ambz (Talk | contribs) uploaded File:Dotplot.png (Syntenic dotplot of E-coli B strain REL606 versus E-coli K12 strain DH 10B)
- 13:18, 2 October 2009 Ambz (Talk | contribs) uploaded File:PastedGraphic-1-.png (Diagram showing WGD events, alpha and beta, before lineage divergence in Arabidopsis.)
- 18:09, 25 September 2009 Ambz (Talk | contribs) uploaded File:Lcs.png (Diagram depicting locally aligned sub-regions of DNA sequences )
- 17:04, 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".)
- 16:34, 23 September 2009 Elyons (Talk | contribs) uploaded File:OrganismView home.png (Initial page for OrganismView)
- 17:43, 21 September 2009 Ambz (Talk | contribs) uploaded File:Otu.png (Diagram depicting evolutionary relationship between orthologs, out-paralogs and in-paralogs.)
- 16:43, 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)
- 12:17, 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)
- 12:12, 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)
- 11:56, 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)
- 11:05, 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))
- 11:00, 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)
- 10:59, 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)
- 15:57, 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)
- 10:46, 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)
- 12:36, 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)
- 12:29, 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)
- 18:46, 25 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)
- 18:44, 25 August 2009 Elyons (Talk | contribs) uploaded File:GEvo-4-at-cp-vv2.png
- 17:14, 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)
- 17:10, 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)
- 17:19, 18 August 2009 Elyons (Talk | contribs) uploaded File:GEvo-setup.png (GEvo's sequence submission setup)
- 16:55, 18 August 2009 Elyons (Talk | contribs) uploaded File:Gobe-interface.png (Image showing GEvo results in Gobe interface)
- 15:38, 12 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView-get feats.png (GenomeView. How to extract features from a genomic view.)
- 15:33, 12 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView-get seq.png (GenomeView with how to get genomic sequence annotated)
- 15:18, 12 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView-information.png (GenomeView's popup information)
- 14:54, 12 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView-navigation.png (GenomeView with navigation buttons annotated.)
- 12:13, 11 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView.png (GenomeView.)
- 12:05, 11 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView-masked.png (GenomeView showing masked genomic regions as purple from the genome of Zea Mays.)
- 12:01, 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.)
- 11:55, 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. )
- 11:55, 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. )
- 11:54, 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.)
- 11:46, 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. )
- 11:45, 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. )
- 11:45, 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.)
- 11:36, 11 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView-CDS.png (GenomeView showing background GC, gene, mRNA, and CDS models. From Arabidopsis genome.)
- 11:36, 11 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView-mRNA.png (GenomeView showing background GC, gene, and mRNA models. From Arabidopsis genome.)
- 11:34, 11 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView-gene.png (GenomeView showing background GC and gene models. From Arabidopsis genome.)
- 11:32, 11 August 2009 Elyons (Talk | contribs) uploaded File:GenomeView-background.png (GenomeView showing AT/GC content)
- 13:01, 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)
- 12:46, 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)
- 12:33, 10 August 2009 Elyons (Talk | contribs) uploaded File:GEvo-show-overlapping.png (GEvo's options for showing overlapping genomic features and HSPs.)
- 14:01, 7 August 2009 Elyons (Talk | contribs) uploaded File:GEvo-with-labels.png (Example GEvo result with contigs, hsp labels, and genomic feature labels drawn.)