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Robert J. Gifford edited this page Apr 11, 2016 · 96 revisions

The DIGS tool provides a computational framework for implementing database-integrated genome-screening (DIGS). The tool is written in PERL. It uses the Basic Local Alignment Search Tool (BLAST) to perform sequence similarity searches, and the MySQL RDBMS to capture results and track progress.

We originally created the DIGS tool for research in the area of ‘paleovirology’, and have primarily used it to screen genome sequence databases for sequences derived from viruses. However, we expect it may have broader utility, and it has been developed with aim of saving others the effort of creating a similar system.

DISCLAIMER

This program may contain bugs, both apparent and less apparent ones. We do not accept responsibility for any problems that arise from use of this software. Use entirely at your own risk.

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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