Tracembler – software for in-silico chromosome walking in unassembled genomes
2007
Tracembler: Software for In-Silico Chromosome Walking
publication
Evidence: moderate
Author Information
Author(s): Dong Qunfeng, Wilkerson Matthew D, Brendel Volker
Primary Institution: Iowa State University
Hypothesis
Can Tracembler effectively assemble genomic regions from unassembled sequence reads?
Conclusion
Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification.
Supporting Evidence
- Tracembler successfully recovered a full-length Chrm2 gene from Rattus norvegicus reads.
- The software identified homologous loci of genes of interest in species with emerging whole genome shotgun reads.
- Tracembler demonstrated high conservation of genes between Medicago truncatula and soybean.
Takeaway
Tracembler is a tool that helps scientists find and piece together DNA sequences from ongoing genome projects, making it easier to study genes.
Methodology
Tracembler uses recursive BLAST searches to identify and assemble matching DNA sequences from the NCBI Trace Archive.
Limitations
The performance of Tracembler is affected by the sequencing depth and the presence of gene duplications.
Digital Object Identifier (DOI)
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