CAFTAN: A Tool for Fast Mapping and Quality Assessment of cDNAs
Author Information
Author(s): del Val Coral, Kuryshev Vladimir Yurjevich, Glatting Karl-Heinz, Ernst Peter, Hotz-Wagenblatt Agnes, Poustka Annemarie, Suhai Sandor, Wiemann Stefan
Primary Institution: DKFZ, German Cancer Research Center
Hypothesis
The efficient use of large cDNA resources requires the development of strategies that can quickly select useful cDNAs from biological and experimental noise.
Conclusion
CAFTAN is a high-throughput sequence analysis tool that quickly predicts the quality of cDNAs, helping researchers select high-quality sequences for further study.
Supporting Evidence
- CAFTAN correctly classified more than 85% of 5950 selected 'known protein-coding' VEGA cDNAs as high quality.
- It identified 80.6% of single exon cDNAs and 85% of multiple exon cDNAs as good.
- CAFTAN provides a fast overview of cDNA quality, supporting the rejection of low-quality sequences.
Takeaway
CAFTAN is like a smart helper that quickly checks thousands of DNA pieces to find the good ones for scientists to study.
Methodology
CAFTAN maps cDNAs to the genome and analyzes their genomic context using various sequence features to classify their quality.
Limitations
The performance of CAFTAN depends on the number of input cDNAs and the overall machine load, and it requires a BLAT mapping output.
Digital Object Identifier (DOI)
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