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Date Name Thumbnail Size Description Versions
13:00, 8 February 2010 GenomeView-GEvo link Glyphs.png (file) 180 KB Screen-shot of GenomeView showing GEvo link glyphs. http://synteny.cnr.berkeley.edu/CoGe/GenomeView.pl?z=5&x=1100000&dsgid=8054&chr=1&sl=1 1
12:55, 8 February 2010 MaizeGDB-CoGe-link.png (file) 232 KB Screenshot of MaizeGDB with link to CoGe. http://gbrowse.maizegdb.org/cgi-bin/gbrowse/maize/?name=chr1:1000000..1200000 1
13:12, 5 February 2010 GenomeView-Other-Feature-Phage.png (file) 56 KB 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. 1
13:08, 5 February 2010 GenomeView-Repeat-regions.png (file) 49 KB 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. 1
13:01, 5 February 2010 GenomeView GEvo-links.png (file) 24 KB GenomeView showing glyphs for links to GEvo. These are displayed when a genomic feature has a link to GEvo for syntenic analysis of syntelogs. 1
12:14, 5 February 2010 GeLo-nucleotides.png (file) 78 KB Example of GeLo graphics using images of nucleotides in the background of the chromosome. 1
19:30, 31 January 2010 Maize-sorghum-cns.png (file) 112 KB GEvo analysis using blastn of a genomic region from sorghum to its two maize syntenic orthologous regions in order to identify CNSs (conserved non-coding sequences). http://tinyurl.com/yek8pdw 1
17:56, 31 January 2010 Maize-sorghum-fractionation.png (file) 146 KB GEvo analysis of sorghum to its two orthologous syntenic regions from maize. http://tinyurl.com/ydbbyeu 1
01:33, 22 January 2010 1923 1922.CDS-CDS.blastn.dag geneorder D20 g10 A5.1-1.w800.png (file) 10 KB Syntenic dotplot by SynMap of two strains of Yersinia pestis. Strain Nepal516 (x-axis); strain Pestoides F. http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=1922;dsgid2=1923;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder 1
01:08, 22 January 2010 1911 1906.CDS-CDS.blastn.dag geneorder D20 g10 A5.1-1.w800.png (file) 8 KB Syntenic dotplot by SynMap of two strains of Yersinia pseudotuberculosis strain. Strain IP 31758 (x-axis); strain YPIII (y-axis). http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=1911;dsgid2=1906;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder 1
23:30, 21 January 2010 3440 3441.CDS-CDS.blastn.dag geneorder D20 g10 A5.1-1.w800.png (file) 14 KB Syntenic dotplot by SynMap of Acidovorax species avenae subsp. citrulli strain AAC00-1 (x-axis) and subspecies JS42 (y-axis). http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=3441;dsgid2=3440;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder 1
22:40, 21 January 2010 Shewanella baltica insertions.png (file) 75 KB GEvo analysis of syntenic regions between two strains of Shewanella baltica showing a variety of insertions. http://tinyurl.com/yc65jyz 1
21:29, 21 January 2010 GEvo Shewanella baltica inversion.png (file) 138 KB GEvo analysis at inversion breakpoints in stains of Shewanella baltica. Inversion is likely to have happened in strain OS155 because it has repeated sequences at the inversion breakpoint. http://tinyurl.com/yhf3gfr 1
21:06, 21 January 2010 Master 2361 2360.CDS-CDS.blastn geneorder D20 g10 A5.w500.png (file) 5 KB Syntenic dotplot by SynMap between strains of Shewanella baltica. http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=2361;dsgid2=2360;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder 1
16:45, 16 January 2010 OrganismView arabid search.png (file) 237 KB OrganismView after searching for "arabid" 1
10:52, 4 January 2010 Arabidopsis tRNA array.png (file) 30 KB Large tandem duplicate gene array of tRNAs from chromosome 1 of Arabidopsis thaliana. This array consists of 27 repeating units of tRNAs, with each unit consisting of three tRNAs that code for a Serine, Tryosine, Tryosine (5'->3'). http://tinyurl.com/yeh 1
13:36, 2 January 2010 FastaView from FeatList.png (file) 165 KB FastaView showing DNA sequences for CDSs exported from FeatList 1
12:47, 2 January 2010 FeatList GenomeView generated.png (file) 308 KB FeatList populated by a link from GenomeView to extract genomic features. 1
12:02, 2 January 2010 Mouse mitochondrial codon usage table.png (file) 185 KB mitochondrion Mus musculus domesticus (western European house mouse) strain AKR/J codon usage table 1
11:38, 2 January 2010 Mouse C57BL-6J chr2 codon usage table.png (file) 182 KB Codon usage table from chromosome 2 of mouse mixed strain C57BL/6J 1
23:18, 1 January 2010 Genomic Feature Annotation.png (file) 138 KB Example genomic feature annotation as presented by FeatView. 1
22:58, 1 January 2010 FeatView At1g01010.png (file) 324 KB FeatView searching for genomic features that have the name "At1g01010". 1
22:55, 1 January 2010 FeatView home.png (file) 73 KB Homepage for FeatView, CoGe's tool for finding genomic features by name or annotation. 1
09:02, 30 December 2009 SynMap DagChainer Options.png (file) 44 KB SynMap's tab for specifying options for DAGChainer 1
20:04, 29 December 2009 SynMap select organisms.png (file) 141 KB Selection boxes for specifying organisms in SynMap 1
19:30, 29 December 2009 Aa usage table for Alkalilimnicola.png (file) 97 KB Amino acid usage table for Alkalilimnicola ehrlichei strain MLHE-1, a high GC gammaproteo bacteria. http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?oid=23562 1
19:28, 29 December 2009 Codon usage table for Alkalilimnicola.png (file) 189 KB Codon usage table for Alkalilimnicola ehrlichei strain MLHE-1, a high GC gammaproteo bacteria. http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?oid=23562 1
19:16, 29 December 2009 Generate codon usage table.png (file) 410 KB Generating a codon usage table with OrganismView 1
17:24, 29 December 2009 System framework.png (file) 80 KB CoGe's web-tools system framework 3
14:58, 29 December 2009 CoGe system design.png (file) 61 KB Overview of CoGe's system design. 1
13:16, 29 December 2009 OrganismView database ids.png (file) 197 KB Screen-shot of OrganismView with CoGe database ids shown and highlighted by red arrows. 1
15:30, 28 December 2009 DH10B-WG3110-Inversion.png (file) 96 KB 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 1
14:15, 28 December 2009 Master 4241 4243.CDS-CDS.blastn geneorder D20 g10 A5.w500.png (file) 7 KB Syntenic dotplot between Escherichia coli K12 substrains DH10B and W3110 showning an inversion. http://tinyurl.com/ya4glwm 1
12:57, 28 December 2009 K12-DH10B-codon-usage.png (file) 188 KB Codon usage table for Eschericia coli K12 DH10B. Generating by OrganismView: http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?oid=24289 1
12:33, 28 December 2009 Gevo-synteny.png (file) 50 KB Intra-genomic synteny from the genome of Arabidopsis thaliana. http://tinyurl.com/noul6b 3
18:56, 22 December 2009 Zm-Sb-6way.png (file) 542 KB 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 1
18:00, 22 December 2009 Maize-sorghum-genome-history.png (file) 29 KB 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. 1
17:50, 22 December 2009 Master 6807 8082.CDS-CDS.blastn geneorder D40 g20 A10.w1200.gene.ks.png (file) 161 KB Syntenic dotplot with Ks coloration of maize versus sorghum. Genes are used for axis metrics. Results can be regenerated at: http://tinyurl.com/y9e778s 1
16:10, 15 October 2009 GEvo-image-parameters-hsp-limit.png (file) 386 KB Setting HSP limits in GEvo 1
16:08, 15 October 2009 GEvo-ra2-cns-discovery.png (file) 203 KB Using blastn in GEvo to identify conserved noncoding sequences for ramora2 in grasses 1
16:07, 15 October 2009 GEvo-blastn.png (file) 112 KB Selecting blastn in GEvo 1
16:06, 15 October 2009 GEvo-identifying-conserved-sequence-ra2.png (file) 102 KB Identifying conserved sequence around ramora2 in GEvo 1
16:04, 15 October 2009 GEvo-change-region-extent.png (file) 43 KB Changing the amount of up and downstream sequence for a sequence submission in GEvo 1
16:02, 15 October 2009 GEvo-add-to-all.png (file) 71 KB Option increase up and downstream sequence to all sequence submissions 1
16:01, 15 October 2009 GEvo-sequence-needs-rc.png (file) 61 KB Identifying a sequence that needs to be reverse complemented in GEvo 1
16:00, 15 October 2009 GEvo-reverse-complement-option.png (file) 77 KB Selecting the reverse complement option for a sequence submission in GEvo 1
15:58, 15 October 2009 GEvo-direct-submission-check.png (file) 140 KB Checking a direct sequence submission in GEvo 1
15:46, 15 October 2009 Ra2-GEvo-result.png (file) 81 KB GEvo result of ra2 in syntenic region between Brachypodium and Rice 1
15:44, 15 October 2009 GEvo-manual-add-sequence.png (file) 115 KB Manually adding a sequence to a GEvo analysis by pasting in a sequence into the sequence submission box. 1
15:43, 15 October 2009 CoGeBlast-HSPTable.png (file) 238 KB HSP table from CoGeBlast 1
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