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 CsuOGS1.0
- Heliconius melpomene Hmel2
- Lerema accius v1.1
- Manduca sexta Msex_1.0
- Papillio glaucus v1.1
- Plodia 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.
- Agraulis vanillae helico2
- Eueides tales helico2
- Heliconius besckei helico2
- Heliconius burneyi helico2
- Heliconius cydno helico2
- Heliconius demeter helico2
- Heliconius elevatus helico2
- Heliconius erato helico2
- Heliconius erato himera helico2
- Heliconius hecale helico1
- Heliconius himera helico1
- Heliconius melpomene helico2
- Heliconius numata helico2
- Heliconius pardalinus helico2
- Heliconius telesiphe helico2
- Heliconius timareta helico2
- Laparus doris helico2
- Neruda aoede helico2
New features
Since Lepbase Ensembl Release 0.5 in February 2015, we have added several new features to the site:
- a standalone blast server using SequenceServer
- an autocomplete search box which makes it easier to search for terms even if you don’t know the exact term or its spelling
- a genome assembly ‘badge’ for visualising genome statistics for each species
- Gene trees made using OrthoFinder for determining homologs, RAxML for building maximum likelihood phylogenetic trees, and TreeFix for species tree reconciliation
- a download page with scaffold fasta, protein fasta, CDS fasta and annotation GFF files for each species
- WebApollo instances for each species at webapollo.lepbase.org to enable manual community-based annotation of these genomes.
Coming soon
- Query driven data downloads
- RFAM annotations
- Variations
- Whole genome alignments