SCARF

SCARF scaffolds and corrects Roche 454 EST assemblies using reference sequences from related species to improve assembly continuity for evolutionary genomics.

Key Features:

• Targeted assembly of Roche 454 ESTs: Focuses specifically on assembling Roche 454 expressed sequence tag (EST) data that are often fragmented and challenging for de novo methods.
• Reference-based orientation and scaffolding: Utilizes a library of reference sequences from related species to orient and scaffold 454 contigs that fail to assemble independently.
• Improved contig continuity: Integrates reference-derived scaffolding to join fragmented contigs into longer, more coherent sequences.
• Accommodation of evolutionary divergence: Applies reference guidance that accounts for sequence divergence among related species during scaffolding.

Scientific Applications:

• Comparative genomics: Supports comparative genomic analyses by producing more complete EST assemblies for cross-species sequence comparisons.
• Cross-species EST expression analysis: Enables assembly of EST data from diverse species to analyze gene expression patterns across taxa.
• Identification of conserved elements and evolutionary inference: Facilitates detection of conserved genetic elements and inference of evolutionary relationships through improved assemblies.

Methodology:

Align Roche 454 EST sequences against a curated library of reference genomes or sequences from related species to orient fragmented contigs and scaffold them into longer assemblies.