News and release notes

Composite cluster capability added to Metazome

We added the ability to combine the gene clusters found in a 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 underclustering, 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 in the help sections on analyzing search results and analyzing BLAST results.

Metazome genomes updated and expanded

Metazome now includes updated Ensembl v41 genomes of twelve species and contains fourteen additional genomes not included in Metazome v1.0. This brings to twenty four 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.

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, for example the Anemone genome.
• BLAST search of individual genomes, for example a Nematostella BLAST search, with links to the Gbrowse view of results in their genomic context.
• Click highlighting of orthologous syntenic genes and shared domains on the 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 the cluster summary page.
• Ability to find all clusters containing particular sets of attributes shared with a given cluster, including gene members and functional assignments.

Minor update to the Metazome interface

We removed the Click Info panel from the Cluster Summary page. The information formerly displayed there, syntenic 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, click on the gene or domain image.