Site Updates and News

01/08/2008 - Minor update to Metazome Interface

We've removed the Click-Info panel from the Cluster Summary page. The information formerly displayed there, systenic gene cluster information and PFAM domain information, is now displayed in pop-up boxes that appear when mousing over a syntenic gene or domain. To freeze the pop-up display and access the hyperlinks inside, simply click on the gene or domain image.

11/12/2023 - Composite cluster capability added to Phytozome

We've added the ability to combine the gene clusters found in single node keyword or BLAST search into a "composite" cluster that can be viewed in a cluster summary page. This is especially helpful when dealing with cases of "under-clustering," where a cohesive gene family is incorrectly broken up into several smaller clusters. Multiple sequence alignments and consensus sequences (used for BLAST searches) are calculated on-the-fly for composite clusters with fewer than 75 members. More information on this feature can be found here and here .

10/23/2023 - Genome set updated and expanded

Metazome now includes updated Ensembl v41 genomes of 12 species, and contains 14 additional genomes not included in Metazome v1.0. This brings to 24 the number of genomes clustered in v2.0.2. The new organisms are:

• Ciona savignyi
• Anopheles gambiae
• Aedes aegypti
• Gasterosteus aculeatus
• Monodelphis domestica
• Oryzias latipes
• Caenorhabditis briggsae
• Branchiostoma floridae
• Bombyx mori
• Nematostella vectensis
• Lottia gigantea
• Tribolium castaneum
• Canis familiaris
• Strongylocentrotus purpuratus

View the info page for more information.

10/23/2023 - New Website

A complete rework of the Metazome website, v2.0.2, has been completed. Navigation has been simplified, synteny viewing features have been enhanced, the individual cluster view display can be customized, and help documentation has been expanded. The genomes of individual organisms can now be searched via BLAST, and their annotations viewed within Gbrowse. In particular,

• Gbrowse genome browsers to view annotations of individual organisms (e.g, Anemone).
• BLAST search of individual genomes (e.g, Nematostella BLAST search), with links to Gbrowse view of results in their genomic context.
• Click highlighting of orthologous syntenic genes and shared domains on cluster summary page.
• Multiple Sequence Alignments are now available within the cluster summary page.
• User-configurable column display.
• Hiding of specific species in search results and cluster summary display.
• Downloading of gene family member sequences and alignments directly from cluster summary page.
• Ability to find all clusters containing particular sets of attributes shared with a given cluster (gene members, functional assignments)