GeneDetective™

Gene modeling and visual exploration of splice variants

GeneDetective includes protein, cDNA and HMM-based gene modeling applications that are processed on the TimeLogic NextEngine™ solutions.

With GeneDetective, you can:

• Map the exon/intron structure of a known transcript
• Find orthologs for large sequences that include many introns
• Study alternatively spliced forms of a gene
• Identify primers for exons in order to study SNPs in the transcribed regions
• Design probes, siRNAs and antisense oligos for alternative forms

GeneDetective internal workflow:

1. ESTs, proteins or hidden Markov models are mapped to genomic DNA using accelerated Tera-BLAST
2. Hits are used to determine genomic boundaries
3. Sequences are re-aligned using a robust variant of the Smith Waterman algorithm which is intron and—for protein sequences—frameshift tolerant to determine optimal alignment
4. Correct splice sites areidentified using splice canonical consensus
5. Multiple sequence alignment output is utilized to generate a graphical, zoomable display, or text-based output ot putative transcripts

GeneDetective's graphical output includes a complete gene model, including short exons and long introns.

The GeneDetective suite is included with the CodeQuest workstations and is an optional DeCypher algorithm suite. GeneDetective complements the DeCypher Tera-BLAST, HMM and Smith-Waterman modules.

GeneDetective™ Search Methods

Download the GeneDetective brochure (pdf, 240k).

Custom Benchmarks

Contact us today for sample GeneDetective benchmarks on your data!