Lepbase Ensembl Release 1.0


Added by Sujai Kumar on October 25th 2015

Lepbase 1.0 went live on October 1, 2015. Several new genomes and features were added to ensembl.lepbase.org, bringing the total number of lepidopteran genomes up to 30, a nice round number.

The new genomes with gene models are:

Chilo_suppressalis_csuogs1Heliconius_melpomeneLerema_accius_v1x1Manduca_sexta_msex1Papilio_glaucus_v1x1Plodia_interpunctella_v1

18 Heliconiine DISCOVAR assemblies by the Heliconius Genome Consortium in collaboration with David Jaffe were also added to Lepbase but these are assemblies without gene models and have not yet been published or verified. Please use blast.lepbase.org to search for your region of interest, and webapollo.lepbase.org to contribute any manual annotations. Please contact James Mallet before using any data from these assemblies in a publication.

New features

Since Lepbase Ensembl Release 0.5 in February 2015, we have added several new features to the site:

  1. a standalone blast server using SequenceServer
    • blast
  2. an autocomplete search box which makes it easier to search for terms even if you don’t know the exact term or its spelling
  3. a genome assembly ‘badge’ for visualising genome statistics for each species
    • badge
  4. Gene trees made using OrthoFinder for determining homologs, RAxML for building maximum likelihood phylogenetic trees, and TreeFix for species tree reconciliation
    • genetree
  5. a download page with scaffold fasta, protein fasta, CDS fasta and annotation GFF files for each species
    • downloads
  6. WebApollo instances for each species at webapollo.lepbase.org to enable manual community-based annotation of these genomes.
    • webapollo

Coming soon

  • Query driven data downloads
  • RFAM annotations
  • Variations
  • Whole genome alignments