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Sequence Data

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Robert J. Gifford edited this page Oct 23, 2024 · 2 revisions

The sequence data in this project are organized 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 Hepadnavirus-GLUE project contains a single NCBI-derived source - ncbi-refseqs - that contains 'master reference' genome sequences for each hepadnavirus species included in this project.

Overview & Installation

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

GLUE Concepts

  1. Project Data Model
  2. Command Layer
  3. Modules
  4. Alignments
  5. Variations
  6. Scripting Layer

Core Project

  1. Schema Extensions
  2. Genome Features
  3. Sequence Data
  4. Reference Sequences
  5. Multiple Sequence Alignments
  6. Constrained Alignment Tree
  7. Phylogenetic Trees

EVE Extension Project

  1. Background
  2. Schema Extensions
  3. Sequences
  4. Reference Sequences
  5. Multiple Sequence Alignments
  6. Paleovirus Nomenclature

Reference

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