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Robert J. Gifford edited this page Jun 24, 2024 · 6 revisions

What has DIGS been used for, and what can it be used for?

DIGS can be used to investigate any genomic feature with sufficient sequence conservation.

The concept for DIGS grew out of early investigations of endogenous retroviruses (ERVs), and has been used to search for ERVs and other kinds of endogenous viral element (EVE).

DIGS has also been used to investigate the evolutionary history of vertebrate genes particularly those that interact with viruses.

Can the DIGS tool be used to screen NGS sequence data?

The DIGS tool is designed for use with assembled sequence data (i.e. not short read data).

The Database Integrated Genome Screening (DIGS) Tool Wiki

Maintained by: R.J. Gifford.

DIGS Tool

  1. Home
  2. Background
  3. Requirements
  4. Installation
  5. Getting Started

Overview

  1. DIGS Concept
  2. Investigation Structure
  3. Exploration Phase
  4. Analysis Phase

Input Components

  1. Target Database (tDB)
  2. Reference Sequence Library (RSL)
  3. Query Sequences (Probes)
  4. Control File

Process

  1. Running a Screen
  2. Project Database
  3. Database Querying
  4. Extending the Project DB Schema
  5. Reclassifying Results
  6. Merging Contiguous Hits

Reference

  1. Example SQL
  2. Archive & Restore Project DBs

Further Information

  1. FAQ
  2. NCBI taxonomy DB
  3. Installation-Guide-for-OS-X

Source Code

  1. Development Approach
  2. Code Summary
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