CRESS DNA virus project overview
Farmed/domesticated species that are afflicted by pathogenic circoviruses: left to right: anseriforme birds (ducks & geese), pigs (family Sulidae), domestic dogs (Canis familiaris), domestic pigeons (Columba livia domestica).
The viral sequence data in this project have been organised into the following sources:
- ncbi refseqs: Genome-length master reference sequences of CRESS DNA virus species representing major lineages, and linked to auxiliary data in tabular format.
- ncbi refseqs-circo: Genome-length reference sequences of representative circovirus species, linked to auxiliary data in tabular format.
- ncbi refseqs-cyclo: Genome-length reference sequences of representative cyclovirus species, linked to auxiliary data in tabular format.
XML-formatted files are downloaded directly from NCBI and are uniquely identified within this project by their GenBank accession numbers.
Project-specific schema extensions
CRESS-GLUE extends GLUE's core schema through the incorporation of a number of additional fields in the sequence table (see here).
Note that CRESS-GLUE also extends the GLUE core schema with an additional table: 'isolate'. This table is linked to the main 'sequence' table via the 'sequenceID' field, and contains isolate-specific information (e.g. species sampled, date and location of sample).
Multiple sequence alignments
Multiple sequence alignment constructed in this study are linked together using GLUE's ‘alignment tree’ data structure. Alignments in the project include:
- A single ‘root’ alignment constructed to represent proposed homologies between representative members of major CRESS virus lineages
- ‘genus-level’ alignments constructed to represent proposed homologies between the genomes of representative members of specific CRESS virus genera.
- ‘Tip’ alignments in which all taxa are derived from a single virus species.
Phylogenetic trees
We used GLUE to implement an automated process for deriving midpoint rooted, annotated trees from the alignments included in our project.
Trees were constructed at distinct taxonomic levels:
- Recursively populated root phylogeny (Rep)
- Genus-level phylogenies