GenSeed

GenSeed performs target-specific DNA assembly using a seed-driven recursive approach to progressively extend initial DNA or protein seed sequences for reconstructing genomic segments and transcripts.

Key Features:

• Implementation: Implemented as a Perl program.
• Seed-driven recursive assembly: Uses a seed-driven recursive strategy that focuses on progressive extension of an initial seed sequence rather than all-against-all comparisons.
• Seed types supported: Accepts predefined seed sequences derived from DNA or protein data, including short sequences from SAGE or proteome projects.
• Target-specific focus: Optimized for assembling specific genomic segments instead of whole genomes or transcriptomes.
• Adaptability to diverse seeds: Handles a diverse array of seed types for different research needs.

Scientific Applications:

• Nuclear gene or segment reconstruction: Reconstruction of nuclear genes or genomic segments from sequencing reads.
• Full-length transcript reconstruction: Assembly of full-length transcripts starting from transcript-derived seeds.
• Extrachromosomal genome reconstruction: Assembly of extrachromosomal genomes using targeted seed extension.

Methodology:

Starting from a predefined DNA or protein seed (including SAGE or proteome-derived short sequences), GenSeed iteratively performs similarity search, read selection, and assembly in recursive cycles to progressively extend and refine the seed-derived assembly.