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EIAV Project Data

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Robert J. Gifford edited this page Dec 3, 2024 · 8 revisions

Genome-Length Reference Sequences

The EIAV extension layer includes a set of genome-length EIAV reference sequences from NCBI Nucleotide, in a source called "ncbi-refseqs-eiav."

Details for each isolate and sequence can be found in the accompanying data file.

A reference phylogeny was generated using maximum likelihood phylogenetic reconstruction, implemented in RAXML. An annotated phylogeny PDF is provided in this repository.

The reference phylogeny defines the following genotypes and subtypes:

  • Genotype American:
  • Genotype Asian:
  • Genotype European1
  • Genotype European2
  • Genotype Spain:
  • Genotype Brazil:
  • Genotype UK:

Nuccore Sequences

The EIAV extension layer contains a regularly updated set of EIAV sequences downloaded from NCBI Nucleotide (GenBank), under the source "ncbi-nuccore-eiav." This set excludes the genome-length references listed above.

These sequences are linked to standardized metadata extracted from GenBank XML using GLUE's GenbankXmlPopulator module. In cases where isolate data are missing from GenBank entries, we have supplemented these fields with values obtained through our EIAV origins investigation. Missing data are added to the Lentivirus-GLUE database using GLUE's textFilePopulator module, configured in this XML file.

Genotype and subtype assignments for all nuccore sequences, previously calculated using a maximum likelihood-based genotyping tool provided with this extension, are also imported from a tabular file.

Additionally, this EIAV extension layer includes comprehensive metadata linked to each EIAV sequence. Metadata categories include:

  • Sequence information (length, publication date)
  • Taxonomic data (genotype, subtype)
  • Isolate data (host species, sampling date, location, isolation source)

Alignment Tree

This extension layer establishes a dedicated alignment tree, rooted on bovine viruses, complementing the genus-level alignment tree created during the Lentivirus-GLUE build.

The alignment tree defines three clade categories:

  1. Subgenus: Equine
  2. Genotype: Follows established nomenclature regarding American, Asian and European clades.

Lentivirus GLUE

Overview & Installation

  1. Home
  2. Background
  3. Requirements
  4. Docker Installation
  5. Native Installation
  6. Usage Overview

Lentivirus Core Project

  1. Overview
  2. Schema Extensions
  3. Core Project Data

SRLV Extension

  1. Background
  2. Project Data
  3. Genotyping Tools

EIAV Extension

  1. Background
  2. Project Data
  3. Genotyping Tools

Primate Extension

  1. Background
  2. Project Data

FIV Extension

  1. Background
  2. Project Data

Bovine Extension

  1. Background

ERV Extension

  1. Background
  2. Schema Extensions
  3. ERV Project Data

The GLUE Framework

User Guide

  1. Project Data Model
  2. Schema Extensions
  3. Modules
  4. Alignments
  5. Variations
  6. Scripting Layer
  7. Freemarker Templates

Command Reference

  1. Command Mode Reference
  2. Mode Non-Specific Commands
  3. Module Type Reference
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