Galign

Galign identifies polymorphisms between Illumina/Solexa sequence reads and an annotated reference genome for genomic-scale polymorphism discovery.

Key Features:

• Parsed-read comparison: Compares parsed Illumina/Solexa sequence reads directly with parsed sequences from an annotated reference genome.
• Alignment approach: Avoids Smith-Waterman matrix-based comparisons by using a direct parsed-sequence comparison algorithm.
• Polymorphism reporting: Produces detailed reports of polymorphism locations, nucleotide substitutions, and predicted amino acid changes.
• Sequencing compatibility: Operates on reads produced by Illumina/Solexa sequencing technology.
• Processing performance: Implements a streamlined algorithm that provides faster analysis while maintaining accuracy comparable to existing prediction programs.

Scientific Applications:

• Polymorphism discovery: Identification of single-nucleotide and other sequence polymorphisms at genomic scale.
• Mutation mapping linked to phenotype: Detection of mutations that can be associated with phenotypic consequences, exemplified by applications in Caenorhabditis elegans.
• Sequence mining across organisms: Use in genomic studies for genetic analysis and variant discovery in diverse organisms.

Methodology:

Requires accessory files derived from an annotated reference genome and compares parsed Illumina/Solexa reads directly to parsed reference sequences rather than using Smith-Waterman matrix-based alignment.