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Exploration Phase

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Robert J. Gifford edited this page Jun 24, 2024 · 3 revisions

Schematic representation of the exploration phase of a DIGS-based investigation.

Here, the genome features being investigated are a set of related genes. In step (1) a sequence from the reference library is selected and used as a 'probe' or 'query' in a BLAST-based search of a chosen target database. In step (2), sequences identified in this search are extracted and classified via BLAST-based comparison to the reference library. These searches provide a way to effectively 'delve in' to genomic databanks and recover related sequences and as such, they provide a means to survey unmapped regions of the genomic 'landscape'. Abbreviations: GF=Genome Feature; FP=False Positive.

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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