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Date Name Thumbnail Size Description Versions
15:41, 15 October 2009 Ra2-CoGeBlast.png (file) 320 KB Configuring CoGeBlast to search multiple grass genomes. 1
15:39, 15 October 2009 NM 001138446.png (file) 69 KB Screen-shot of NM_001138446 from NCBI 1
18:26, 14 October 2009 Master 6871 4242.genomic-CDS.blastn geneorder D100 g50 A5.w2000.ass.png (file) 32 KB 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. 1
18:22, 14 October 2009 Master 6871 4242.genomic-CDS.blastn geneorder D100 g50 A5.w2000.png (file) 30 KB Comparison of a de novo assembled E. coli genome sequenced using the whole genome shotgun approached without any bac-ends to order contigs. 1
16:04, 23 September 2009 OrganismView Example Search.png (file) 224 KB Example screen-shot from OrganismView when searching for any organism's whose name contains "arabid". 1
15:34, 23 September 2009 OrganismView home.png (file) 101 KB Initial page for OrganismView 1
15:43, 21 September 2009 K12-MG1655-DH10B-syn dotplot.png (file) 10 KB 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 1
11:17, 16 September 2009 CoGe-Analysis-Network.png (file) 71 KB 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 1
11:12, 16 September 2009 CoGe-Front-End.png (file) 176 KB 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 1
10:56, 16 September 2009 K12-HGT.png (file) 329 KB 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 1
10:05, 30 August 2009 SynPlot-Chr1-At-v-Al.png (file) 362 KB (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) 2
10:00, 30 August 2009 Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.hist-1.png (file) 7 KB (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 2
09:59, 30 August 2009 Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.png (file) 115 KB (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 3
14:57, 28 August 2009 GEvo-At-Al.png (file) 1,021 KB 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 1
17:46, 25 August 2009 GEvo-4-at-cp-vv.png (file) 1.17 MB 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 2
16:14, 25 August 2009 Genome-phylogeny-At-Cp-Vv.png (file) 58 KB 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 1
16:19, 18 August 2009 GEvo-setup.png (file) 102 KB GEvo's sequence submission setup 1
15:55, 18 August 2009 Gobe-interface.png (file) 142 KB Image showing GEvo results in Gobe interface 1
14:38, 12 August 2009 GenomeView-get feats.png (file) 143 KB GenomeView. How to extract features from a genomic view. 1
14:33, 12 August 2009 GenomeView-get seq.png (file) 136 KB GenomeView with how to get genomic sequence annotated 1
14:18, 12 August 2009 GenomeView-information.png (file) 305 KB GenomeView's popup information 1
13:54, 12 August 2009 GenomeView-navigation.png (file) 153 KB GenomeView with navigation buttons annotated. 1
11:13, 11 August 2009 GenomeView.png (file) 173 KB GenomeView. 1
11:05, 11 August 2009 GenomeView-masked.png (file) 10 KB GenomeView showing masked genomic regions as purple from the genome of Zea Mays. 1
11:01, 11 August 2009 GenomeView-Unsequenced.png (file) 13 KB GenomeView with show unsequenced genomic regions as orange from the genome of Carica papaya. 1
10:55, 11 August 2009 GenomeView-wobbleGC3.png (file) 14 KB GenomeView with CDS wobble GC content colored yellow for ~50% GC content in codon wobble positions. Chlamydomonas reinhardtii mitochondria genome. 1
10:55, 11 August 2009 GenomeView-wobbleGC2.png (file) 14 KB GenomeView with CDS wobble GC content colored red for low GC content in codon wobble positions. Chlamydomonas reinhardtii chloroplast genome. 1
10:54, 11 August 2009 GenomeView-wobbleGC1.png (file) 23 KB GenomeView with CDS wobble GC content colored green for high GC content in codon wobble positions. Chlamydomonas reinhardtii genome. 1
10:46, 11 August 2009 GenomeView-pseudogene-2.png (file) 20 KB GenomeView showing many neighboring pseudogenes (orange-red) in the genome of Sulfolobus islandicus strain L.S.2.15. 1
10:45, 11 August 2009 GenomeView-pseudogene.png (file) 18 KB GenomeView pseudo gene (orange-red) in the genome of Sulfolobus islandicus strain L.S.2.15. 1
10:45, 11 August 2009 GenomeView-rRNA.png (file) 18 KB 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. 1
10:36, 11 August 2009 GenomeView-CDS.png (file) 20 KB GenomeView showing background GC, gene, mRNA, and CDS models. From Arabidopsis genome. 1
10:36, 11 August 2009 GenomeView-mRNA.png (file) 20 KB GenomeView showing background GC, gene, and mRNA models. From Arabidopsis genome. 1
10:34, 11 August 2009 GenomeView-gene.png (file) 15 KB GenomeView showing background GC and gene models. From Arabidopsis genome. 1
10:32, 11 August 2009 GenomeView-background.png (file) 12 KB GenomeView showing AT/GC content 1
12:01, 10 August 2009 GEvo-local-dup-show-overlap.png (file) 116 KB 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 1
11:46, 10 August 2009 GEvo-local-dup-no-show-overlap.png (file) 149 KB 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 1
11:33, 10 August 2009 GEvo-show-overlapping.png (file) 154 KB GEvo's options for showing overlapping genomic features and HSPs. 1
13:01, 7 August 2009 GEvo-with-labels.png (file) 42 KB Example GEvo result with contigs, hsp labels, and genomic feature labels drawn. 1
13:00, 7 August 2009 GEvo-contigs-and-labels.png (file) 144 KB Shows where the options are for drawing labels and contigs for GEvo results. 1
17:32, 6 August 2009 GeLo-example.png (file) 94 KB Example of GeLo's graphics with different genomic "stuff" labeled. 1
17:22, 6 August 2009 Diploidization-cartoon.png (file) 112 KB 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 1
17:17, 6 August 2009 Fractionation-cartoon.png (file) 101 KB 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 1
16:30, 4 August 2009 At-Cp-Retention.png (file) 180 KB   1
16:21, 4 August 2009 At-Cp-Fractionation.png (file) 366 KB 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 1
11:08, 4 August 2009 GEvo-links.png (file) 290 KB Screen-shot of the results of a GEvo analysis with links for regenerating and saving the analysis labeled. 1
14:22, 14 July 2009 Crab spider.jpg (file) 48 KB Yellow Crab spider 1
14:20, 14 July 2009 100px-Nsf1.jpg (file) 6 KB NSF logo 1
22:30, 12 May 2009 Master 3068 8.CDS-CDS.blastn geneorder D20 g10 A5.w2000.ks.hist.png (file) 7 KB Histogram of Ks values for the image master_3068_8.CDS-CDS.blastn_geneorder_D20_g10_A5.w2000.ks.png 1
21:47, 12 May 2009 Grape-tomato-synteny.png (file) 130 KB 250kb region of tomato aligned with a 500kb region of grape. Regenerated at http://tinyurl.com/qjpcvv 1
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