Release Notes

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:
    1. 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.
    2. The Multiple Sequence Alignment tool allows users to align protein or DNA sequences filtered from the PaVE database or uploaded.
    3. 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.