Tracembler

Tracembler performs recursive BLAST searches of NCBI Trace Archive whole genome shotgun reads and assembles matching traces with CAP3 to reconstruct local genomic regions and identify homologous genes.

Key Features:

• Recursive Database Searches: Uses BLAST iteratively to identify matching sequences from the NCBI Trace Archive starting from user-supplied DNA or protein seed sequences.
• Sequence Assembly: Assembles BLAST-matching reads into contigs using the CAP3 program based on significant sequence overlaps.
• Gene Identification: Facilitates identification of homologous loci and genes from assembled contigs to explore genetic architecture across species.
• Flexible Search Parameters: Supports stopping criteria such as maximum number of queries, maximum rounds of recursion, or termination when no new matches are found.

Scientific Applications:

• Local genome reconstruction: Reconstructs local genome assemblies when early whole genome shotgun coverage at a locus is sufficient to produce reliable contigs.
• Chrm2 gene recovery: Recovered the full-length Chrm2 gene with upstream and downstream regions from Rattus norvegicus reads.
• Microsyntenic homolog identification: Using two adjacent Medicago truncatula genes as seeds, identified a contig likely corresponding to the microsyntenic homologous locus in soybean.

Methodology:

Performs iterative BLAST searches where sequences identified in one round serve as queries for subsequent rounds and assembles BLAST-matching reads into contigs with CAP3 based on overlaps, continuing until predefined stopping criteria (maximum queries/rounds or no new matches) are met.