Sequence Data

The sequence data in this project are organised into multiple distinct sources.

Each source contains data in either GenBank XML or plain FASTA format.

The type of data is indicated by the name of the source (all GenBank XML sources contain 'ncbi' in the name).

GenBank XML files are imported into this project directly from NCBI GenBank using an appropriately configured version of GLUE's GenBank importer module.

The core Flavivirid-GLUE project contains a single NCBI-derived source - ncbi-refseqs - that contains 'master reference' genome sequences for each flavivirid species included in this project.

Where possible, we prefer to use sequences obtained via GenBank since it represents the principle source of published nucleotide sequence data.

However, FASTA sources can also be used in GLUE, making it straightforward to expand private instances of this GLUE project with unpublished sequences.

Genbank sequences are uniquely identified within GLUE projects by their GenBank accession numbers.
Sequences included in this project are linked to auxiliary data in tabular format.

We defined 'master' reference sequences to represent recognised flavivirid genera/subgenera, as follows:

Subgroups of Genus Flavivirus

• Mosquito-borne flavivirus group 2: Yellow fever virus 1 (NC_002031)
• Mosquito-borne flavivirus group 1: Dengue virus 1 (NC_001477)
• Tick-borne flaviviruses: Powassan virus (NC_003687)
• No-known vector group 1: Apoi virus (NC_003676)
• No-known vector group 2: Sokuluk virus (NC_026624)
• Dual-host insect-specific flavivirus group: Lammi virus (NC_024806)
• Mpulungu flavivirus group: Mpulungu flavivirus (LC582740)
• Classical insect-specific flavivirus group: Kamiti river virus (NC_005064)
• Crustacean flavivirus group: Crangon crangon flavivirus (MK473878)

Other Flaviviridae genera

• Tamanavirus: Tamana bat virus (NC_003996)
• Jingmenvirus: Jingmen tick virus segment 1 (NC_024113)
• Jingmenvirus: Jingmen tick virus segment 3 (NC_024114)
• Pestivirus: Bovine viral diarrhea virus 1 (NC_001461)
• Pesti-like 1 (PL2): Soybean cyst nematode virus 5 (NC_024077)
• Pesti-like 2 (PL2): Shuangao lacewing virus 2 (NC_028373)
• Hepacivirus: Hepatitis C virus (NC_004102)
• Pegivirus: Human pegivirus 2 (NC_027998)

We explicitly defined the locations of genome features on master reference sequences using GLUE commands (see here).