Release Notes
Oct 23rd, 2024
New additions
- 2 new reference HPV genomes, HPV230 and HPV231
- 9 new non-reference HPV genomes, HPV-m7299, HPV-m7372,HPV-m7221,HPV-m8923,HPV-m7269,HPV-m7350,HPV-m7334,HPV-m7570,HPV-m7424
- 117 new animal papillomavirus genomes
- AmexPV1, Ambystoma mexicanum (Axolotl)
- AplaPV3, Anas platyrhynchos (Mallard duck)
- AsmexPV1, Astyanax mexicanus (Mexican tetra)
- AsylPV1, Apodemus sylvaticus (Wood mouse)
- BbarPV1, Barbastella barbastellus (Barbastelle bat)
- BsplPV1, Betta splendens (Siamese fighting fish)
- CPV25, 26, 27, 28, 29, 30, 31, 32, 33, Canis familiaris (Domestic dog)
- CcarPV1,PV2, PV3, PV4, PV5, PV6, Caracal caracal (Caracal)
- ClatPV1, Canis latrans (Coyote)
- ClivPV1, Columba liviat Rock pigeon)
- CrupPV1, Coryphaenoides rupestris (Roundnose grenadier)
- CsemPV1, Cynoglossus semilaevis (Chinese tongue sole)
- CxCPV1, Carassius auratus x cyprinus carpio (Hybrid fish- goldfish x common carp)
- DleuPV2, Delphinapterus leucas (Beluga whale)
- ElPV2, Enhydra lutris (Sea otter)
- FcaPV8, PV9, PV10, Felis domesticus (Domestic cat)
- GgulPV1, Gulo gulo (Wolverine)
- GmorPV1, PV2, Gadus morhua (Atlantic cod)
- HlarPV1, Hipposideros larvatus (Intermediate leaf-nosed bat)
- HlepPV1, PV2, PV3x, Hydrurga leptonyx (Leopard seal)
- LleiPV1, PV2, Leptobrachium leishanense (Leishan spiny toad)
- LsvePV1, Luscinia svecica (Bluethroat (bird))
- LwPV8, PV9 PV10, PV11, PV12, PV13, Leptonychotes weddellii (Weddell seal)
- MconPV1, Mops condylurus (Angolan free-tailed bat)
- MsilPV1, Myotis siligorensis (Himalayan whiskered myotis)
- MungPV1, Meriones unguiculatus (gerbil)
- PV-7377-sorex, PV-7569-sorex, PV-8217(sorex species, Shrew)
- PV-7585-mus (mouse)
- PV-7615, PV-8112 rhinolophus (horseshoe bat)
- PV-763, PV-7683 (rodent)
- PV-7687, PV-8160, PV-8005 (molossus sp, free tail bat))
- PV-7808-bat (bat)
- PV-7812-myodes (Myodes species, vole)
- PV-GD2016, PV-GD2018, PV-SC2018 (bat)
- PV-JX2020 (fish)
- PguaPV1, Podarcis guadarramae (Guadarrama wall lizard)
- PparPV1, PV2, PV3, Panthera pardus (Leopard)
- PtirPV1, Panthera tigris tigris (Bengal tiger)
- RaffPV1, PV2, PV3, PV4, PV5, PV6, Rhinolophus affinis (Intermediate horseshoe bat)
- RfPV2, PV3, PV4, PV5, PV6, PV7,PV8 Rhinolophus ferrumequinum (Greater horseshoe bat)
- RjiePV1, PV2,PV3, Rana jiemuxiensis (Jiemuxi frog)
- RpusPV1, PV2, PV3, Rhinolophus pusillus (Least horseshoe bat)
- RsinPV1, PV2, PV3, PV4, PV5, Rhinolophus sinicus (Chinese horseshoe bat)
- SaPV2, Sparus aurata, (Gilt-head bream)
- SchiPV1, PV2, Sousa chinensis, (Indo-pacific humpback dolphin)(
- SkuhPV1, PV2, PV3, PV4, Scotophilus kuhlii (Lesser asiatic yellow bat)
- TmelPV1, PV2, Taphozous melanopogon (Black-bearded tomb bat)
- TpacPV1, PV2, PV3, PV4, Tylonycteris pachypus (Lesser bamboo bat)
- TrobPV1, PV2, PV3, PV4, Tylonycteris robustula (Greater bamboo bat)
- XbirPV1, Zalophus californianus (Sealion)
- 22 new protein structures:
- HPV16, HPV18, E6 proteins/peptides
- HPV16, E7 proteins/peptides
- HPV16 L1 peptides
- HPV4, HPV18 L2 peptides
April 5th, 2024
New additions
- Added the blastn-short option for blastn and the blastp-short option for blastp. See the BLAST+ features documentation for details.
July 26th, 2023
Fixes
- Added missing metadata for 46 Human Papillomavirus genomes
May 19th, 2023
New additions
- 2 new reference HPV genomes, HPV228 and HPV229
- 1 new non-reference HPV genome, HPV-mJDFY01
- Corrected classification of HPV177 from Alphapapillomavirus-7 to Alphapapillomavirus-11
- 57 new animal papillomavirus genomes
- AalbPV1, Atelerix albiventris papillomavirus type 1 (Four-toed hedgehog)
- AmPV5, Ailuropoda melanoleuca papillomavirus type 5 (Giant panda)
- AplaPV2, Anas platyrhynchos papillomavirus type 2 (Mallard)
- BPV30,31,32,33,34,35,36,37,38,39,40,41,42,43,44, Bovine papillomavirus types (Domestic cow)
- CPV24, Canine papillomavirus type 24 (Domestic dog)
- CstrPV1,2,3, Centropristis striata papillomavirus type 1, 2, 3 (Sea Bass)
- DleuPV1, Delphinapterus leucas papillomavirus type 1 (Beluga whale)
- EaPV3, Equus asinus papillomavirus type 3 (African wild ass)
- EbonPV1,2, Eumops bonariensis papillomavirus type 1 and 2 (Dwarf bonneted bat)
- EcPV10, Equus caballus papillomavirus 10 (Domestic horse)
- EhPV4, Eidolon helvum papillomavirus 4 (Straw-coloured fruit bat)
- ErugPV1, Eptesicus regulus papillomavirus type 1 (Southern forest bat)
- FcaPV7, Felis catus papillomavirus 7 (Domestic cat)
- MaegPV3,4,5,6, Melanogrammus aeglefinus associated papillomavirus type 3,4,5,6 (Haddock)
- MfoiPV1, Martes foina papillomavirus type 1 (Beech marten)
- MjavPV1,2,3, Manis javanica papillomavirus type 1,2,3 (Sunda pangolin)
- MrPV1, Myotis ricketti papillomavirus 1 (Ricketts big-footed bat)
- NasiPV1,2,3,4,5,6, Neophocaena asiaeorientalis papillomavirus 1,2,3,4,5,6 (Narrow-ridged finless porpoise)
- PtroPV1, Pan troglodytes papillomavirus 1 (Chimpanzee)
- PV-fi100-fish, Fish associated papillomavirus fi100 (fish)
- PV-HMU5-rodent, PV-HMU6-rodent, Rat associated papillomavirus HMU5, HMU6 (Rat)
- PV-wesgulfec-fish, Wesgulfec associated papillomavirus (Unidentified)
- RmarPV1, Rhinella marina papillomavirus type 1 (Cane toad)
- SglaPV1, Silurus glanis papillomavirus type 1 (Wels catfish)
- TberPV1, Trematomus bernacchii papillomavirus type 1 (Emerald rockcod)
- TmPV5, Trichechus manatus papillomavirus type 5 Caribbean manatee
- TperPV1, Taphozous perforatus papillomavirus 1 (Egyptian tomb bat)
- VvarPV1,2, Varecia variegata papillomavirus 1,2 (Black-and-white ruffed lemur)
- 10 new protein structures:
- HPV16, HPV18, HPV35 E6 proteins
- HPV16, HPV58, MmuPV1 L1 proteins
Fixes
- Fixed GFF3 formatting error
April 20, 2022
PaVE version 2.0 release
We re-wrote PaVE from the ground up. After almost 10 years, it was time. We moved PaVE out of it's aging Java framework and into a new Python framework called Flask. We hope that we've maintained everything you loved about PaVE, and that we've added some new features you find nice to have. Here's everything we changed:
- Full GUI update:
- Refreshed the look-and-feel. Most things should still be right where you left them, but we did move a few things around. The phylogenetic tree is now under "Analyze," and we've recategorized the help and support pages, for example.
- Replaced JsPhyloSVG with phylotree.js (a D3 library) for viewing the phylogenetic tree.
- Replaced JSMol with Mol*, providing a richer set of functionality when viewing structures
- Display the tree on the L1 typing tool results page.
- Provide an interactive viewer to display the multiple sequence alignment results.
- Updated the tools:
- Replaced Cobalt with MAFFT for multiple sequence alignments (note, this may affect the results of the L1 typing tool, which is dependent on the alignment for classification)
- Upgraded to the latest version of BLAST+
- Upgraded to the latest version of PAUP* for phylogenetic tree generation
New additions
- Two new movies: one showing the viral minichromosome packaged into a viral capsid, and one showing how the viral genome partitions during cell division.
New features
- Genomes can now be downloaded in GFF3 format from the Search Database page.
- Added a new 3D Viewer that provides interactive visualizations that explore key aspects of HPV structure and lifecycle.
Jun 14th, 2021
New additions
- 1 new non-reference HPV genome.
- A previous non-reference genome became HPV227
- 10 new animal papillomavirus genomes:
- BPV28 and BPV29, Bos taurus papillomavirus types 28 and 29(domestic cattle)
- CdPV3, Camelus dromedarius papillomavirus type 3 (Arabian camel)
- CpenPV1 and PV2, Callithrix penicillata papillomavirus type 1 and 2 (Black tufted marmoset)
- FcaPV6, Felis catus papillomavirus 6 (domestic cat)
- OjohPV1,Okapia johnstoni Papillomavirus type 1 (Okapi or zebra giraffe)
- TbraPV2 and 3, Tadarida brasiliensis papillomavirus type 2 and 3 (Mexican free tailed bat)
- BPV-mTAPV-lsx, Tick-associated papillomavirus lsx isolate TAPV-lsx (tick associated virus, likely BPV30)
- 8 new protein structures: HPV16 and HPV58 L1, and HPV31 E6.
- New images of MmuPV1 and EdPV infection
Jan 13th, 2020
New additions
- 27 new HPV genomes (22 HPV reference and 5 non-reference genomes). Some previous non-reference genomes became reference types in this update.
- 4 new animal papillomavirus genomes:
- EcPV9, Equus caballus papillomavirus type 9 (domestic horse)
- HfrePV1, Hemidactylus frenatus papillomavirus type 1 (the common house gecko)
- HfrePV2, Hemidactylus frenatus papillomavirus type 2 (the common house gecko)
- TbraPV1,Tadarida brasiliensis papillomavirus type 1 (Mexican free tailed bat). *4 new protein structures: HPV16, 18, and 49 E6 proteins in complex with structures in complex with various LxxLL motifs.
May 23rd, 2019
New additions
- 147 new HPV genomes (3 HPV reference and 143 non-reference genomes)
- 22 new animal papillomavirus genomes:
- AchePV1 (Chevrier’s field mouse)
- AplaPV1 (Mallard)
- BPV25 (Cow)
- BPV26 (Cow)
- BPV27 (Cow)
- BgPV1 (Yak)
- CPV21 (Dog)
- CPV22 (Dog)
- CPV23 (Dog)
- EaPV2 (Donkey)
- EdPV2 (North American porcupine)
- FarcPV1 (Atlantic puffin)
- LcamPV1 (red snapper)
- LsmiPV1 (American Herring Gull)
- LwiePV1 (Margay)
- MaegPV1 (Haddock)
- MaegPV2 (Haddock)
- MfuPV2 (Japanese Macaque)
- OjohPV1 (Okapi)
- RnPV4 (Norwegian rat)
- TbelPV1 (Tree shrew)
- TbelPV2 (Tree shrew)
- 8 new or updated protein structures: BPV1 E2 DNA binding domain and various HPV L1 pentamers
- New annotation for E1 binding sites
New features
- Updated L1 typing tool
May 7th, 2018
New additions
- 16 new HPV genomes (14 HPV types and 2 non-reference genomes)
- 13 new animal papillomavirus genomes:
- BPV24 (domestic cow)
- LwPV1-7 (Weddel seal)
- MmoPV1 (Velvety free-tailed bat)
- RtiPV2 (Javan rusa deer)
- ScPV1 (Atlantic canary)
- ScPV2 (Atlantic canary)
- TtPV8 (Bottle-nose dolphin)
- TtPV9 (Bottle-nose dolphin)
- 6 new protein structures: HPV16 capsids, and HPV16 and HPV59 pentamers bound to Fabs and heparin
- Transcript map for MmuPV1, mouse papillomavirus
- Link to Expert Views on HPV Infection
September 15th 2017
New additions
- 84 new HPV genomes (83 non-reference genomes)
- 12 new animal genomes:
- AMPV1 from Giant Panda
- AMPV2 from Giant Panda
- AMPV3 from Giant Panda
- AMPV4 from Giant Panda
- BPV22 from the domestic cow
- BPV23 from the domestic cow
- EhPV2 from the straw-colored fruit bat
- EhPV3 from the straw-colored fruit bat
- FcaPV5 from the domestic cat
- OaPV4 from the domestic sheep
- PaPV2 from the Adelie penguin
- SsPV2 from the domestic pig
- Two new protein structures, HPV16 L1 VLP particles in complex with heparin
January 30th 2017
New additions
- Lots of new animal genomes in this update. BPV16, 17, 18, 19, 20, 21, CEPV1, CPV18, CPV19, EcPV8, GcPV1, PpuPV1, and SaPV1 (a fish papillomavirus)
- Two new protein structures, HPV59 L1 pentamers
- Updated E8 and E10 protein pages
- Updated links
Sept 2nd, 2016
New additions
- 1 new genome added
- Updated annotation for the newly designated E10 ORF (formerly named E5 or E8). E10 is an ORF that either overprints the E6 ORF, or is encoded in this region (in the absence of an E6 gene) in a small number of papillomaviruses.
May 27th, 2016
New additions
- Nine new genomes: AgPV1, CePV2, CPV17, CPV20, MfuPV1, RtiPV1 and HPV157, 158, 205
- Updated sequences: MsPV1, HPV5, HPV165
- Variants: newly released accession numbers added to Variant Genomes Table and NCBI Variant Searches
- Protein Structure Database: Nine new structures added- E1 helicase domain; E6/E6AP/p53 ternary complex; HPV16 capsids in complex with antibodies
December 22, 2015
New additions
- RalPV1, RnPV3 and three human non-reference genomes added to the PaVE database
- New transcript map for SfPV1 (CRPV) from Frank Stubenrauch
- Imageviewer has 41 new images from Patty Pesavento and Kevin Keel
- HeLa integration site epigenetic data updated on JBrowse
September 8, 2015
New additions
- 12 new genomes have been incorporated into the PaVE database
May 6, 2015
New features
- New Circular Genome Viewer
- New Table of Common Variant Genomes
March 16, 2015
New additions
- VvPV1 genome has been incorporated into the PaVE database
- Updated several URR and E8^E2 annotations
January 16, 2015
New features
- Dynamic phylogenetic tree generation for PaVE reference proteins
- Locus viewer enhanced
Fixes
- URR sequence joins corrected
December 1, 2014
New features
- Upgraded Cobalt from 2.0.1 to 2.0.2 (used in MSA)
Fixes
- Fixed translation (8 entries) and transcripts (7 entries), removed one duplicate feature (E6* in MfPV10REF)
October 30, 2014
New additions
- Additional Transcript maps were added
- 3 new genomes incorporated
October 1, 2014
New additions
- Download 3D printable models for PV structures
- New images added to the Image Viewer
New features
- Interactive and zoomable Phylogenetic tree
September 17, 2014
New additions
- Epigenetic data from HPV18 integration site in HeLa cells
August 15, 2014
New additions
- 43 new genomes have been incorporated into the PaVE database
May 30, 2014
New features
*The PaVE GUI (graphical user interface) has been reorganized to be more intuitive and logical. We hope that you like it!
December 6, 2013
New additions
- The PaVE database has been updated to include 33 new genomes and additional gene/protein annotations for all genomes
- Additional HPV and CPV images have also been added to the Image Viewer
July 7, 2013
PaVE version 1.1 release
- Three new tools have been added to the new release of PaVE:
- An L1 taxonomy tool allows users to determine whether they might have a new PV type before submission to the Animal or Human PV Reference Center.
- The Multiple Sequence Alignment tool allows users to align protein or DNA sequences filtered from the PaVE database or uploaded.
- A new Image Viewer contains gross and microscopic images of papillomavirus infection.
- In collaboration with Elsevier, PaVE has spearheaded a Special Issue of Virology about the functional genomics of Papillomaviruses. Each article in the Special Issue provides an in-depth, unbiased and encyclopedic overview of different aspects of papillomavirus genomics and proteomics, written by experts in the papillomavirus field. The main aim of each article is to completely document details about viral proteins, cis-elements, evolution, and disease. This Special Issue is intended to be a companion resource to the PaVE website and will serve as an important reference resource for the scientific community. You can visit the blog site for this special issue at http://www.virologyhighlights.com/?p=144.