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Annotation Statistics and Version

Statistics | Annotation Metrics | Curation Metrics | Version

 

Current Statistics (Release 6.8.2 ; Web Updates):

This release of the VBRC database comprises virus information on:

7
Families
30
Genera
209
Species
4958
Strains
70732
Genes

Annotation Metrics (Release 6.8.2):

Metric Arenaviridae Bunyaviridae Filoviridae Flaviviridae Paramyxoviridae Poxviridae Togaviridae
General Statistics (arena)(bunya)(filo)(flavi)(para)(pox)(toga)
Genera 1 4 2 3 9 10 1
Species 23 50 6 53 39 24 15
Strains 117 1048 33 3054 305 112 120
Refs in PubMed (via MeSH) 2798 4098 916 28411 23274 11507 8880
Max Num. proteins/genome 6 8 10 15 12 328 13
Gene Assignments (arena)(bunya)(filo)(flavi)(para)(pox)(toga)
GenBank total proteins 316 2016 249 25296 1696 20748 792
VBRC total proteins 449 2618 250 39660 2359 22289 1351
VBRC updated 10 64 3 3539 142 661 369
VBRC new 133 609 2 14207 668 1657 571
new & updated by mol. type
      gene 13 109 4 685 810 2135 64
      mature protein 130 562 1 16978     845
      poly protein   2   83     30
      pseudo gene           183 1
Poxviridae Specific (arena)(bunya)(filo)(flavi)(para)(pox)(toga)
Gene Prediction
      microRNAs           1  
Regulatory Motifs, from Literature
      lit. transcription promoters           145  
      lit. gene temporality           235  
      # of Pubmed Refs           37  
Regulatory Motifs, Putative
      putative transcription promoters           7842  
      putative gene temporality           6354  
RefSeq update submissions (arena)(bunya)(filo)(flavi)(para)(pox)(toga)
      RefSeq update submissions           1  
      db_xref links     24 51      
      LinkOut links     25 54      
Functional Assignments (arena)(bunya)(filo)(flavi)(para)(pox)(toga)
Interpro hits
      genes with IP hits 266 1047 193 4180 1211 19176 886
      % genes with IP hits 59% 39% 77% 10% 51% 86% 65%
      GO assignments 320 1542 163 3035 1749 18163 2183
      genes w/ GO term 265 992 81 1616 1087 7516 536
      % genes w/ GO term 59% 37% 32% 3% 46% 33% 39%
      unique GO terms 10 34 6 15 29 160 18
Immune Epitopes (arena)(bunya)(filo)(flavi)(para)(pox)(toga)
IEDB (Epitope DB) links
      genes with epitopes 413 1131 230 35298 963 16866 319
      % genes w/ epitope 91% 43% 92% 85% 40% 75% 23%
Structure Predictions (arena)(bunya)(filo)(flavi)(para)(pox)(toga)
Protein motifs
      coiled coil 121 342 80 513 495 1468 85
      signal peptide 184 847 87 19406 795 3312 299
      trans-membrane sig. 171 974 40 20625 736 5366 482
      ProSite hit 96 288 19 1575 396 3829 207
PDB hits
      100% identity 16   10 724 59 199 194
      homologs   13 35 6718 171 5317 514
Ortholog Clusters (arena)(bunya)(filo)(flavi)(para)(pox)(toga)
VOC (Viral Orthologous Clusters)
      genes assigned 449 2618 250 39660 2359 22289 1351
      % genes assigned 100% 100% 100% 95% 100% 100% 100%

Literature Curation Metrics (Release 6.8.2):

Family
      Genus
            Species		 genes per genome genes curated % genes num. anno­tations bio. proc. GO ids cell comp. GO ids mol func. GO ids total GO ids assign­ed papers
Bunyaviridae
      Phlebovirus
            Rift Valley fever virus segment L
                  strain ZH-548 1 1 100% 26 6 8 4 18 8
                  strain Clone_13 1 1 100% 3 0 0 0 0 3
                  strain MP-12 1 1 100% 4 0 0 0 0 4
                  strain ZH-501 1 1 100% 40 8 9 5 22 15
            Rift Valley fever virus segment M
                  strain ZH-501 5 5 100% 171 53 21 6 80 27
                  strain MP-12 5 4 80% 37 0 0 0 0 14
                  strain ZH-548 5 4 80% 19 0 0 0 0 5
            Rift Valley fever virus segment S
                  strain ZH-548 2 2 100% 69 8 11 10 29 16
                  strain MP-12 2 2 100% 37 4 2 2 8 16
                  strain pp13_74HB59 2 1 50% 3 0 0 0 0 3
                  strain ZH-501 2 2 100% 153 27 17 10 54 30
Filoviridae
      Ebolavirus
            Reston ebolavirus strain Pennsylvania-Groseth 8 8 100% 206 21 20 9 50 36
            Zaire ebolavirus strain Mayinga-Volchkov 10 10 100% 697 105 34 63 202 143
      Marburgvirus
            Lake Victoria marburgvirus strain Musoke 7 7 100% 424 64 49 40 153 69
            Lake Victoria marburgvirus strain Popp 7 7 100% 101 8 2 4 14 21
Flaviviridae
      Flavivirus
            Dengue virus type 1 strain Nauru Island Western Pacific 45AZ5 14 14 100% 411 43 14 32 89 146
            Dengue virus type 2 strain 16681-Kinney 14 14 100% 995 101 66 88 255 236
            Dengue virus type 3 strain D3-H-IMTSSA-SRI-2000-1266 14 14 100% 157 10 3 20 33 60
            Dengue virus type 4 strain rDEN4 14 14 100% 257 34 10 22 66 77
            West Nile virus strain NY99 14 11 79% 754 75 79 75 229 144
      Hepacivirus
            Hepatitis C virus genotype 1a strain H77 12 12 100% 1523 183 133 96 412 402
Poxviridae
      Orthopoxvirus
            Vaccinia virus strain Copenhagen 273 187 68% 2732 25 7 12 44 475

Version History:

Click for schema history.
Release 6.8.2 (Web Updates)
Date:
 18 Jun 2009Release of the Dengue virus Genotyping application. See: http://www.denguedb.org/submitGenotypeRequest.aspx?type=Dengue
Curator:
 John Osborne; Don Dempsey
Release 6.8.1 (Web Updates)
Date:
 15 May 2009New ID search interface; updated genome and gene search interfaces; updated genome and gene map displays; updated gene records; and updated Viral Orthologous Cluster (VOCs) descriptions
Curator:
 Elizaveta Karpova; Melissa Da Silva; Don Dempsey; Curtis Hendrickson; John Osborne; Jim Moon
Release 6.8 (Data Updates)
Date:
 03 Apr 2009New data release. Note that the N- and C- terminal ends of the mature peptides for many of the hepatitis C virus genomes have been adjusted to fix a problem with the identification of polyprotein protease cleavage sites.
Curator:
 John Osborne; Curtis Hendrickson; Melissa Da Silva
Release 6.7.1 (Web Updates)
Date:
 03 Mar 2009Release of the Hepatitis C virus Genotyping application. See: http://hcvdb.org/submitGenotypeRequest.aspx
Curator:
 John Osborne; Don Dempsey
Release 6.7 (Data Updates)
Date:
 12 Sep 2008New data release
Curator:
 John Osborne; Curtis Hendrickson; Don Dempsey; Elizaveta Karpova; Jim Moon; Melissa Da Silva; Mary Wagner; Kate Kudy
Release 6.6.1 (Web Updates)
Date:
 25 Aug 2008Redesign of Blast Analysis tool to link results to sequences in the database to allow display of genosubtype, publications or other information.
Curator:
 John Osborne
Release 6.6 (Data Updates)
Date:
 07 Jul 2008New data release.
Curator:
 John Osborne; Melissa Da Silva; Shankar Changayil
Release 6.5.1 (Web And Data Updates)
Date:
 20 Jun 2008Release of the DengueDB, www.denguedb.org web site
Curator:
 Brett Pickett; Cathy Galloway; Curtis Hendrickson; Don Dempsey; Elizaveta Karpova; Jim Moon; John Osborne; Melissa Da Silva; Tamara Crutchley
Release 6.5 (Data Updates)
Date:
 07 Jun 2008New data release.
Curator:
 Melissa Da Silva; Shankar Changayil; John Osborne
Release 6.4.1 (Web And Data Updates)
Date:
 22 May 20081. Addition of protein interaction data from the Protein Resource Centers
2. Addition of web-based context-sensitive help
3. Web page enhancements and bug fixes
Curator:
 Shankar Changayil; Don Dempsey; Jim Moon; Ritu Arora; John Osborne; Curtis Hendrickson

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